Load Libraries

# libraries used for analysis
library(edgeR)
library(limma)
library(quadprog)
library(ruv)

# libraries required for graphics
library(ggplot2)
library(reshape2)
library(EDASeq)
library(RColorBrewer)
library(VennDiagram)
library(data.table)
library(dplyr)
library(stringr)
library(knitr)
library(pheatmap)


wd = "./"
colors <- c("#0571b0", "#ca0020")

Load our data

We first produce a matrix of read counts after aligning to both the Human and Plasmodium falciparum 3D7 reference genome. Subread’s featureCounts program is then used to allocate reads to gene features using the gff file PlasmoDB-12.0_Pfalciparum3D7.gff from PlasmoDB. For both Subread programs the default options are used.

setwd(wd)
# # Next subreads featureCounts was used to allocate reads to genes. This
# was saved for re-use files <-
# Sys.glob('/home/users/allstaff/tonkin-hill.g/all_gene_analysis/alignment/*.sam')
# fc_genes_aligned_w_Pfhuman_withoutVivax <- featureCounts(files, annot.ext
# = './data/PlasmoDB-12.0_Pfalciparum3D7.gff' , isPairedEnd=TRUE,
# isGTFAnnotationFile=TRUE, GTF.attrType='ID', GTF.featureType='gene' ,
# nthreads=15)

# Load gene ID mappings which we use later on.
geneID_mappings <- fread("./data/geneID_mappings.txt", data.table = FALSE, stringsAsFactors = FALSE)
trim <- function(x) gsub("^\\s+|\\s+$", "", x)
s <- str_split(as.character(geneID_mappings$`[Previous ID(s)]`), ",")
geneID_mappings <- data.frame(current = rep(geneID_mappings$`[Gene ID]`, sapply(s, 
    FUN = length)), old = unlist(s))
geneID_mappings$old <- str_trim(geneID_mappings$old)

# Load read counts (if featureCounts has been run previously)
load("./data/fc_genes_with_all_samples_aligned_human_Pf_WithOutVivax_subread_uH.RData")
fc2 <- fc_genes_aligned_w_Pfhuman_withoutVivax
t <- fc2$counts

# Rename samples to something more sensible colnames(t) <-
# gsub('alignment\\.sam','',colnames(t)) colnames(t) <-
# gsub('.*vivax\\.','',colnames(t)) colnames(t) <- gsub('_S.*','',
# colnames(t))
fc2$counts <- t

x <- DGEList(counts = fc2$counts, genes = fc2$annotation)

Initial filter

We next filter out genes that do not have sufficient coverage across our samples for reliable estimates to be made.

setwd(wd)
before <- nrow(x$counts)
keep <- rowSums(cpm(x) > 2) >= 10
x <- x[keep, , keep.lib.sizes = FALSE]

We require that there are at least 2 reads per million for at least 10 samples in order for a gene to be included in the analysis. This reduced the number of genes being considered from 5777 to 4144.

Remove low depth samples

setwd(wd)
bplot <- melt(colSums(x$counts))
colnames(bplot) <- c("Read.Counts")
bplot$Sample <- rownames(bplot)

gg <- ggplot(bplot, aes(x = factor(Sample), y = Read.Counts)) + geom_bar(stat = "identity")
gg <- gg + theme_bw() + scale_y_sqrt(breaks = c(0, 10000, 1e+06, 1e+07, 1e+08))
gg <- gg + theme(axis.text.x = element_text(size = 12, angle = 90), axis.text.y = element_text(size = 12, 
    angle = 0), axis.title = element_text(size = 14, face = "bold"))
gg <- gg + labs(x = "Sample", y = "Read Count")
gg <- gg + geom_hline(aes(yintercept = 1e+06), col = "red")

x$counts <- x$counts[, !grepl("SFD1|SFM9|SFC\\.025", colnames(x$counts))]
filt.annnotation <- fc2$annotation[fc2$annotation$GeneID %in% rownames(x$counts), 
    ]
dge <- DGEList(counts = x$counts, genes = filt.annnotation)

gg

Samples SFD1, SFM9 and SFC.025 were not sequenced to a sufficient depth to be reliable and thus are removed.

Remove drug treated samples

Samples SFU2 and SFU3 were drug treated and are removed. We repeated the analysis of the all gene DGE omitting a few patients who had anti-malarial treatments in preceding months. The patients omitted are: SFC 023, SFM007, IFM 012 and IFM 021.

x$counts <- x$counts[, !grepl("SFU2|SFU\\.3", colnames(x$counts))]
x$counts <- x$counts[, !grepl("SFC\\.023|SFM\\.7|IFM12|IFM21", colnames(x$counts))]
filt.annnotation <- fc2$annotation[fc2$annotation$GeneID %in% rownames(x$counts), 
    ]
dge <- DGEList(counts = x$counts, genes = filt.annnotation)

Now we take the log transform of our sample counts (RPKM) to estimate the proportion of different stages present.

setwd(wd)
our_log_rpkm <- rpkm(dge)
our_log_rpkm <- log2(1 + our_log_rpkm)

Estimate Contributions from Different Life-cycle Stages

Load Data

To estimate the proportion of different life-cycle stages in each of our samples we require a reference data set. Su et al provide such a reference. They performed RNA-seq at two gametocyte stages, an ookinete stage and four time points of erythrocytic stages representing ring, early trophozoite, late trophozoite, and schizont. As we do not expect any ookinete stage parasites we discarded this reference. The data was downloaded from PlasmoDB and as such read counts were reported in RPKM. To handle outlying counts in a sensible manner a log2 transformation of the RPKM values was performed. This was also done for our gene counts. By next fitting a mixture model we can estimate the proportion of different parasite stages that make up our samples.

setwd(wd)
su_rpkm <- read.csv("./data/ rpkm_7SexualAndAsexualLifeStages_suetal.csv", header = TRUE, 
    sep = ",")

# ignore the Ookinete profile as this should be absent from our data.
su_rpkm$Ookinete <- NULL
rownames(su_rpkm) <- su_rpkm$ID
su_rpkm$ID <- NULL

# take the log transform of the data which helps to manage outlier genes.
su_log_rpkm <- log2(1 + su_rpkm)

Mixture Model

Given a set of stages \(S\) and a set of genes \(g_i: i\in \{1,...,N\}\) we want to minimise

\[ \sum_{i=1}^N \left( g_{i,sample} - \sum_{s \in S} \pi_s g_{i,s} \right)^2 \]

Subject to constraints

\[ \sum_{s\in S} \pi_s = 1 \]

\[ \pi_s > 0 \]

Here \(\pi_s\) is proportion of stage \(s\) that is attributed to having contributed to our sample. This model was fit using R’s solve.QP function.

setwd(wd)
findMix <- function(Y, X) {
    X[is.na(X)] <- t(replicate(ncol(X), apply(X, 1, mean, na.rm = T)))[is.na(X)]
    Rinv <- solve(chol(t(X) %*% X))
    C <- cbind(rep(1, ncol(X)), diag(ncol(X)))
    b <- c(1, rep(0, ncol(X)))
    d <- t(Y) %*% X
    qp <- solve.QP(Dmat = Rinv, factorized = TRUE, dvec = d, Amat = C, bvec = b, 
        meq = 1)
    sol <- qp$solution
    sol[sol < 1e-10] <- 0
    return(sol)
}

Calculate Sample Life-Cycle Profiles

We fit this mixture model to each of our samples in turn. The results are then plotted. A column represents each sample in the plot below. As we are fitting proportion parameters each columns values must add to 1 over the 5 stages. Note that we have also combined the estimated proportions for the gametocyte samples into one gametocyte variable. The columns are coloured by phenotype.

setwd(wd)
# First get the intersection of the genes for the two datasets and order
# them by rowname.
inter <- intersect(rownames(our_log_rpkm), rownames(su_log_rpkm))

O <- our_log_rpkm[rownames(our_log_rpkm) %in% inter, ]
O <- O[order(rownames(O)), ]
S <- su_log_rpkm[rownames(su_log_rpkm) %in% inter, ]
S <- S[order(rownames(S)), ]

# Now lets fit some samples!
ourPlotData <- data.frame()
for (i in 1:ncol(O)) {
    mix <- findMix(O[, i], as.matrix(S))
    ourPlotData <- rbind(ourPlotData, data.frame(sample = rep(colnames(O)[i], 
        ncol(S)), stage = colnames(S), proportion = mix))
}

# Organise the results.
ourPlotData$stage <- gsub("Gametocyte.*", "Gametocyte", ourPlotData$stage)
ourPlotData <- aggregate(proportion ~ sample + stage, data = ourPlotData, FUN = sum)
ourPlotData <- within(ourPlotData, stage <- factor(stage, levels = c("Ring", 
    "Early.Trophozoite", "Late.Trophozoite", "Schizont", "Gametocyte")))
ourPlotData$phenotype <- ifelse(substring(ourPlotData$sample, 1, 1) == "I", 
    "non-severe", "severe")

# Make a pretty plot.
gg <- ggplot(ourPlotData, aes(x = factor(sample), y = proportion, fill = factor(phenotype))) + 
    geom_bar(stat = "identity")
gg <- gg + scale_fill_manual(values = c(`non-severe` = "#2c7bb6", severe = "#d7191c"))
gg <- gg + facet_wrap(~stage, ncol = 1)
gg <- gg + theme_bw()
gg <- gg + theme(axis.text.x = element_text(size = 12, angle = 90), axis.text.y = element_text(size = 12, 
    angle = 0), axis.title = element_text(size = 14, face = "bold"), strip.text.x = element_text(size = 16, 
    face = "bold"))
gg <- gg + labs(x = "Sample", y = "Proportion", fill = "Stage")
gg <- gg + theme(legend.text = element_text(size = 14))
gg <- gg + theme(legend.key.size = unit(0.25, "in"))
gg <- gg + theme(legend.title = element_text(size = 16, face = "bold"))
gg <- gg + guides(fill = guide_legend(title = "Phenotype"))
gg

Investigate Differential Expression

We now perform the Voom transformation on our count matrix. Prior to the transformation we use TMM normalisation to account for the different library sizes present in our sample. TMM was chosen as it is more robust to outliers. From the Voom variance trend it is evident that there are a number of genes that have both high variability and high expression. After looking at some of the main offenders these were identified to be influenced by staging in the parasite. Consequently it is important to account for life-cycle stage when conducting the differential expression analysis.

options(width = 150)
setwd(wd)
categories <- as.factor(substring(rownames(dge$samples), 1, 1))
dge <- calcNormFactors(dge, method = "TMM")
dge$samples$group <- categories
design <- model.matrix(~group, data = dge$samples)

v <- voom(dge, design = design, plot = TRUE)

PCA Normalising for Library Size

The PCA plot below indicates that accounting for library size alone does not cope with the impact of life-cycle stages. Notably SFC21 is clearly an outlier and was identified in the mixture model as containing later stage parasites as well as gametocytes. IFM14 is also slightly separate in the PCA plot and was identified as having a proportion of Schizont stage parasite present.

setwd(wd)
plotPCA(v$E, col = colors[categories], cex = 0.8, isLog = TRUE)

Further the Relative Log Expression (RLE) plot below suggests that there is something different about SFC21 as well as highlighting IFM060 as being different.

setwd(wd)
plotVoomRLE <- function(E, colours) {
    mn <- apply(E, 1, median)
    rle <- data.frame(sweep(E, MARGIN = 1, STATS = mn, FUN = "-"))
    boxplot(rle, col = colours, outline = FALSE, las = 2, ylim = c(-7, 7))
    abline(h = 0, col = "black")
}
plotVoomRLE(v$E, colors[categories])

PCA Normalising for Library Size, Ring, Gametocyte and Schizont effects.

To investigate the impact of life-cycle stages in our analysis we fit a linear model using limma’s removeBatchEffect. Initially ring, gametocyte and schizont parameters were fit along with the disease phenotype factor. This was because for the most part the Trophozoite stages could be represented by accounting for these stages as they would be present implicitly in the model.

The PCA indicates that we have dealt with the outlying SFC21 sample as well as other less outlying samples such as IFM14 which showed a proportion of Schizont stage parasites in the mixture model. Unfortunately due to the low number of samples that have proportions of Schizont and Gametocytes estimating differential differential expression in severe disease becomes impossible. This is because there is insufficient data to estimate these stage parameters and consequently the uncertainty in the model is too high to find significant differences between severe and non-severe disease.

setwd(wd)
covs <- data.frame(v$design[, 2])
ourPlotData$phenotype <- NULL
c <- dcast(ourPlotData, sample ~ ..., value.var = "proportion")
covs <- merge(covs, c, by.x = 0, by.y = "sample")

colnames(covs) <- c("sample", "disease", colnames(c)[2:ncol(c)])
rownames(covs) <- covs$sample
covs$sample <- NULL
covs <- covs[match(colnames(v$E), rownames(covs)), ]
stopifnot(colnames(v$E) == rownames(covs))
# head(covs)

covs <- covs[, c(1, 2, 5, 6)]
# head(covs)

mod = model.matrix(as.formula(paste("~", paste(colnames(covs), collapse = " + "), sep = "")), data = covs)

norm_counts_ring <- removeBatchEffect(v$E, covariates = mod[, 3:ncol(mod)], design = mod[, 1:2])
plotPCA(norm_counts_ring, col = colors[categories], cex = 0.8, isLog = TRUE)

The RLE plot also suggests we have dealt with SFC21 however accounting for these stages does not seem to have accounted for the differences we see in the IFM060 sample. The mixture model did not identify IFM060 as being noticeably different from the other samples and consequently it is likely that there is some other unknown factor impacting on its expression.

setwd(wd)
plotVoomRLE(norm_counts_ring, col = colors[categories])

PCA Normalising for Library Size and Ring Stage Effects

We then investigate the impact of only accounting for the Ring stage parameter in the model. This gives us more power with which to identify differential expression related to severe disease. However, from the PCA plot below it is clear that accounting for Ring stage alone is insufficient and fails to adequately deal with SFC21.

setwd(wd)
covs <- covs[, c(1, 2)]

mod = model.matrix(as.formula(paste("~", paste(colnames(covs), collapse = " + "), sep = "")), data = covs)

norm_counts_ring <- removeBatchEffect(v$E, covariates = mod[, 3:ncol(mod)], design = mod[, 1:2])
plotPCA(norm_counts_ring, col = colors[categories], cex = 0.8, isLog = TRUE)

We are however able to identify differentially expressed genes in this less parameterised model. The summary of results accounting only for the Ring stage variable are given below. This test was performed using the limma-Voom pipeline. Ideally we would be able to keep both the power in out tests and account for the remaining unwanted factors. To achieve this we make use of RUV-4 to estimate dummy variables that represent multiple unknown factors of unwanted variation.

setwd(wd)
stopifnot(colnames(dge) == rownames(mod))
v2 <- voom(dge, design = mod, plot = FALSE)
fit <- lmFit(v2, mod)
fit <- eBayes(fit, robust = TRUE)

summary(de1 <- decideTests(fit, adjust.method = "BH", p.value = 0.05))
##    (Intercept) disease Ring
## -1          81      18 1265
## 0          681    4069 1734
## 1         3382      57 1145

Estimate Unwanted Factors of Variation

To cope with the outlier samples such as SFC21 whilst retaining statistical power we estimate factors of unwanted variation using RUV-4.
RUV-4 requires a set of control genes which are believed to be relatively unaffected by the condition of interest, in our case this is disease severity. RUV-4 is however fairly robust to the choice of control genes.
We chose to use the 1000 genes found to have the highest p-values in the experiment of Vignali et al as controls. The experiment of Vignali et al looked at differences in expression between pregnancy associated malaria and childhood malaria. Although this is not the same association we are investigating it was considered close enough to perform adequately as a source of control genes. Further an analysis using SVA which does not require controls and rather estimates them empirically was found to produce similar results with only 5 out of 119 genes found using SVA missing from the RUV-4 approach. Further RUV-4 attempts to recover some variation that may be lost in the vanilla SVA approach when the factor of interest (severe disease) correlates with an unwanted factor. Consequently it leads to a higher number of differentially expressed genes being found. It was also thought that having an independently sourced set of control genes was preferable to empirically deriving such a set.

setwd(wd)
contol_genes_vignali <- read.table("./data/contol_genes_vignali.txt", quote = "\"")

ctrl_vignali <- geneID_mappings$current[geneID_mappings$old %in% contol_genes_vignali$V1]
length(ctrl_vignali)
## [1] 1009
empirical_controls <- ctrl_vignali[0:length(ctrl_vignali)]
empirical_controls <- rownames(v$E) %in% empirical_controls

categoriesRUV <- categories
categoriesRUV <- data.matrix(as.numeric(categoriesRUV == "S"))
ring <- data.matrix(mod[, c(1, 3)])
genes <- data.matrix(t(v$E))

ruv <- RUV4(genes, categoriesRUV, empirical_controls, 3, Z = ring)

modRUV = cbind(mod, ruv$W)

norm_counts_ring_ruv <- removeBatchEffect(v$E, covariates = modRUV[, 3:ncol(modRUV)], design = modRUV[, 1:2])

Note that although we used 1000 genes from the experiment of Vignali et al only 533 were found in our reduced expression matrix.

The PCA plot below indicates that we have dealt with most of the problems due to staging. Here we have included the Ring stage proportion from the mixture model as well as three factors of unwanted variation estimated using RUV-4.

setwd(wd)
plotPCA(norm_counts_ring_ruv, col = colors[categories], cex = 0.8, isLog = TRUE)

The RLE plot also indicates that we have succesfully dealt with most of the staging issues. Both SFC21 and IFM14 have reasonable box plots. Moreover, IFM060 has a nicer boxplot indicating that in using RUV-4, not only have we dealt with staging issues, we have also accounted for some other unknown confounding factors that would have impacted our results. The variation in each sample has also been reduced which is indicated in the reduced height of the boxplot whiskers. Finally, the results were found to be relatively robust to the removal of the outlier samples such as SFC21 and IFM14. Consequently, this approach seems to succesfully deal with both life-cycle staging issues and other unknown impacting factors.

setwd(wd)
plotVoomRLE(norm_counts_ring_ruv, colors[categories])

Identify DE Genes using Limma and Voom

We now use the limma-voom pipeline, with the robust ebayes option which handles dispersion outliers. This was done to further ensure our results were less likely to be affected by outlier samples. Multiple testing correction was performed using the Benjamini-Hochberg approach.

setwd(wd)
stopifnot(colnames(dge) == rownames(modRUV))
v2 <- voom(dge, design = modRUV, plot = F)
fit <- lmFit(v2, modRUV)
fit <- eBayes(fit, robust = TRUE)
s <- summary(de2 <- decideTests(fit, adjust.method = "BH", p.value = 0.05))
s
##    (Intercept) disease Ring               
## -1          91      72 1393 1621 1101  478
## 0          548    4033 1450 1651 2070 3114
## 1         3505      39 1301  872  973  552

Overall 111 genes were found to be differentially expressed between severe and non-severe cases of malaria with a false dicovery rate threshold of 0.05.

A good check for validity of our model it to look at the distribution of the resulting p-values. If everything is okay we would expect a uniform distribution except near \(p=0\) where we would hope to see a spike. The barplot below indicates this is what we see which is helpful in affirming that we have done okay in removing unwanted variation without negatively impacting on the variation due to the variable of interest (diseas severity).

setwd(wd)
top_ring_ruv <- topTable(fit, coef = 2, p.value = 0.1, sort.by = "p", number = Inf, adjust.method = "BH", confint = TRUE)
hist <- data.frame(topTable(fit, coef = 2, number = Inf))
gg <- ggplot(hist, aes(x = P.Value)) + geom_histogram(binwidth = 0.01)
gg <- gg + theme_bw()
gg <- gg + theme(axis.text.x = element_text(size = 12), axis.text.y = element_text(size = 12, angle = 0), axis.title = element_text(size = 12, face = "bold"))
gg <- gg + labs(x = "P value", y = "Count")
gg

Results table

Below is a table of genes that were found to be differentially expressed, ordered by their respective p-values. The 95% confidence intervals are given with the estimated LFC as well as the BH adjusted p-values and the log-odds that the gene is differentially expressed. Here we report for interest sake all genes up to a adjusted p-value threshold of 0.1.

setwd(wd)
# Load additional gene information
GeneAnnotationPlasmoDB <- fread("./data/GeneAnnotationPlasmoDB.txt", data.table = FALSE, na.strings = "N/A")

# First lets import some additional gene information to make a nicer table
GeneAnnotationPlasmoDB <- GeneAnnotationPlasmoDB[, colnames(GeneAnnotationPlasmoDB) %in% c("[Gene ID]", "[Product Description]", "[Gene Name or Symbol]")]
top_ring_ruv <- merge(top_ring_ruv, GeneAnnotationPlasmoDB, by.x = 0, by.y = "[Gene ID]", all.x = TRUE)
top_ring_ruv <- top_ring_ruv[with(top_ring_ruv, order(adj.P.Val)), ]

# Now print the table
top_ring_ruv$P.Value <- format(top_ring_ruv$P.Value, scientific = TRUE, digits = 3)
top_ring_ruv$adj.P.Val <- format(top_ring_ruv$adj.P.Val, scientific = TRUE, digits = 3)
kable(top_ring_ruv[, c(2:4, 6:ncol(top_ring_ruv))], digits = 3)
GeneID Chr Start Strand Length logFC CI.L CI.R AveExpr t P.Value adj.P.Val B [Product Description] [Gene Name or Symbol]
9 PF3D7_0115700 Pf3D7_01_v3 607390 - 7504 -1.695 -2.671 -0.718 4.472 -5.551 2.64e-06 5.48e-03 4.608 erythrocyte membrane protein 1, PfEMP1 VAR
14 PF3D7_0202000 Pf3D7_02_v3 103385 - 2412 -2.232 -3.132 -1.331 14.042 -5.745 2.34e-06 5.48e-03 4.793 knob-associated histidine-rich protein KAHRP
271 PF3D7_1255200 Pf3D7_12_v3 2241271 - 7692 -1.490 -2.030 -0.951 4.566 -5.412 4.07e-06 5.63e-03 4.220 erythrocyte membrane protein 1, PfEMP1 VAR
23 PF3D7_0223500 Pf3D7_02_v3 916352 - 7297 -1.139 -1.932 -0.345 5.205 -4.963 1.63e-05 8.42e-03 2.968 erythrocyte membrane protein 1, PfEMP1 VAR
31 PF3D7_0316600 Pf3D7_03_v3 669302 - 1572 -1.407 -1.944 -0.870 10.248 -5.170 9.43e-06 8.42e-03 3.434 formate-nitrite transporter FNT
37 PF3D7_0400100 Pf3D7_04_v3 28706 + 8972 -1.593 -1.921 -1.266 4.810 -5.026 1.34e-05 8.42e-03 3.139 erythrocyte membrane protein 1, PfEMP1 VAR
156 PF3D7_0900100 Pf3D7_09_v3 20080 + 7806 -1.462 -2.010 -0.915 4.673 -5.057 1.22e-05 8.42e-03 3.224 erythrocyte membrane protein 1, PfEMP1 VAR
189 PF3D7_1023600 Pf3D7_10_v3 987358 - 2791 -2.045 -3.030 -1.060 -0.122 -4.980 1.54e-05 8.42e-03 2.487 conserved Plasmodium protein, unknown function NA
243 PF3D7_1223900 Pf3D7_12_v3 972710 - 684 -2.228 -4.701 0.246 2.658 -4.936 1.86e-05 8.58e-03 2.764 50S ribosomal protein L24, putative NA
142 PF3D7_0809100 Pf3D7_08_v3 459312 + 7256 -1.773 -3.635 0.089 3.226 -4.884 2.08e-05 8.60e-03 2.665 erythrocyte membrane protein 1, PfEMP1 VAR
4 PF3D7_0106000 Pf3D7_01_v3 255775 - 2769 1.185 0.199 2.172 1.476 4.664 4.07e-05 1.23e-02 1.920 conserved Plasmodium protein, unknown function NA
36 PF3D7_0324900 Pf3D7_03_v3 1030822 - 7433 -1.274 -2.295 -0.254 3.988 -4.507 6.54e-05 1.23e-02 1.680 erythrocyte membrane protein 1, PfEMP1 VAR
40 PF3D7_0404600 Pf3D7_04_v3 247731 + 12417 -1.457 -1.770 -1.145 7.604 -4.502 7.43e-05 1.23e-02 1.515 conserved Plasmodium membrane protein, unknown function NA
45 PF3D7_0412700 Pf3D7_04_v3 561667 - 7676 -1.440 -2.188 -0.692 4.841 -4.530 6.09e-05 1.23e-02 1.753 erythrocyte membrane protein 1, PfEMP1 VAR
85 PF3D7_0600600 Pf3D7_06_v3 29618 - 1867 -1.681 -2.462 -0.901 3.049 -4.700 3.63e-05 1.23e-02 2.155 erythrocyte membrane protein 1 (PfEMP1), exon 2 VAR
105 PF3D7_0632800 Pf3D7_06_v3 1374797 - 7831 -1.240 -1.577 -0.904 4.681 -4.544 5.85e-05 1.23e-02 1.791 erythrocyte membrane protein 1, PfEMP1 VAR
107 PF3D7_0703100 Pf3D7_07_v3 121414 + 543 0.985 0.194 1.777 3.582 4.477 7.15e-05 1.23e-02 1.588 conserved Plasmodium protein, unknown function NA
120 PF3D7_0712600 Pf3D7_07_v3 566726 - 7583 -1.748 -2.417 -1.079 3.429 -4.685 3.80e-05 1.23e-02 2.144 erythrocyte membrane protein 1, PfEMP1 VAR
133 PF3D7_0800100 Pf3D7_08_v3 21361 + 7293 -1.596 -2.257 -0.936 4.508 -4.513 6.58e-05 1.23e-02 1.687 erythrocyte membrane protein 1, PfEMP1 VAR
136 PF3D7_0802000 Pf3D7_08_v3 146089 + 4194 -1.266 -1.753 -0.778 9.188 -4.509 6.90e-05 1.23e-02 1.558 glutamate dehydrogenase, putative GDH3
175 PF3D7_1000100 Pf3D7_10_v3 28490 + 7675 -1.339 -1.639 -1.040 4.505 -4.569 5.41e-05 1.23e-02 1.861 erythrocyte membrane protein 1, PfEMP1 VAR
204 PF3D7_1105100 Pf3D7_11_v3 226065 + 354 -1.063 -1.589 -0.536 9.705 -4.600 5.10e-05 1.23e-02 1.799 histone H2B H2B
216 PF3D7_1123100 Pf3D7_11_v3 909366 + 6959 -0.597 -0.908 -0.287 9.103 -4.524 6.21e-05 1.23e-02 1.610 calcium-dependent protein kinase 7 CDPK7
231 PF3D7_1200100 Pf3D7_12_v3 16973 + 7525 -1.592 -2.227 -0.957 4.052 -4.609 4.80e-05 1.23e-02 1.964 erythrocyte membrane protein 1, PfEMP1 VAR
296 PF3D7_1344800 Pf3D7_13_v3 1796274 + 1436 -0.768 -1.123 -0.413 6.260 -4.560 5.58e-05 1.23e-02 1.803 aspartate carbamoyltransferase ATCase
248 PF3D7_1228800 Pf3D7_12_v3 1169557 - 9630 -0.657 -1.727 0.414 6.788 -4.415 8.63e-05 1.38e-02 1.365 WD repeat-containing protein, putative NA
84 PF3D7_0532400 Pf3D7_05_v3 1312471 + 1684 -1.315 -1.774 -0.856 8.118 -4.393 9.77e-05 1.40e-02 1.251 lysine-rich membrane-associated PHISTb protein LyMP
102 PF3D7_0626200 Pf3D7_06_v3 1058666 - 1257 1.643 0.966 2.319 2.878 4.387 9.37e-05 1.40e-02 1.321 conserved Plasmodium protein, unknown function NA
244 PF3D7_1224000 Pf3D7_12_v3 974372 + 1170 -1.670 -3.718 0.378 2.666 -4.378 9.63e-05 1.40e-02 1.298 GTP cyclohydrolase I GCH1
322 PF3D7_1414200 Pf3D7_14_v3 564024 - 1224 0.818 0.286 1.349 5.924 4.353 1.04e-04 1.43e-02 1.233 conserved Plasmodium protein, unknown function NA
198 PF3D7_1100100 Pf3D7_11_v3 24160 + 7439 -1.288 -1.828 -0.748 4.713 -4.310 1.18e-04 1.58e-02 1.148 erythrocyte membrane protein 1, PfEMP1 VAR
6 PF3D7_0109700 Pf3D7_01_v3 379149 - 658 -1.423 -2.847 0.001 4.127 -4.269 1.33e-04 1.73e-02 1.040 rRNA biogenesis protein RRP36, putative RRP36
71 PF3D7_0519500 Pf3D7_05_v3 801450 - 7678 -0.942 -1.573 -0.311 7.017 -4.157 1.86e-04 2.09e-02 0.640 carbon catabolite repressor protein 4, putative CCR4
153 PF3D7_0830300 Pf3D7_08_v3 1290240 - 1167 1.591 1.299 1.884 2.023 4.162 1.83e-04 2.09e-02 0.694 sporozoite invasion-associated protein 2 SIAP2
168 PF3D7_0925300 Pf3D7_09_v3 1019164 - 1740 2.109 1.367 2.850 0.173 4.158 1.86e-04 2.09e-02 0.535 proline–tRNA ligase, putative aPRS
193 PF3D7_1028000 Pf3D7_10_v3 1160031 + 3391 -0.991 -1.656 -0.326 6.363 -4.158 1.86e-04 2.09e-02 0.667 methyltransferase, putative NA
285 PF3D7_1316600 Pf3D7_13_v3 691014 + 3112 -1.262 -1.567 -0.958 6.456 -4.192 1.76e-04 2.09e-02 0.726 choline-phosphate cytidylyltransferase CCT
117 PF3D7_0711700 Pf3D7_07_v3 511950 - 7476 -1.151 -1.908 -0.394 4.402 -4.081 2.34e-04 2.50e-02 0.533 erythrocyte membrane protein 1, PfEMP1 VAR
287 PF3D7_1318300 Pf3D7_13_v3 753910 + 5523 -1.051 -1.390 -0.712 5.766 -4.078 2.36e-04 2.50e-02 0.476 conserved Plasmodium protein, unknown function NA
166 PF3D7_0917800 Pf3D7_09_v3 734629 + 1314 1.808 1.549 2.068 1.383 4.051 2.55e-04 2.64e-02 0.378 conserved Plasmodium protein, unknown function NA
58 PF3D7_0500100 Pf3D7_05_v3 20929 + 7528 -1.287 -1.826 -0.748 3.399 -4.023 2.77e-04 2.68e-02 0.384 erythrocyte membrane protein 1, PfEMP1 VAR
224 PF3D7_1135300 Pf3D7_11_v3 1381015 - 1230 1.219 0.684 1.754 2.281 4.032 2.70e-04 2.68e-02 0.380 conserved Plasmodium membrane protein, unknown function NA
238 PF3D7_1213100 Pf3D7_12_v3 576417 - 164 -2.305 -2.853 -1.757 2.312 -4.036 2.79e-04 2.68e-02 0.339 U1 spliceosomal RNA NA
286 PF3D7_1316900 Pf3D7_13_v3 701047 - 2877 0.669 0.039 1.299 7.752 4.007 2.90e-04 2.73e-02 0.185 conserved Plasmodium protein, unknown function NA
242 PF3D7_1223400 Pf3D7_12_v3 941125 + 5621 -0.766 -2.537 1.005 11.206 -3.995 3.01e-04 2.77e-02 0.101 phospholipid-transporting ATPase, putative NA
124 PF3D7_0713600 Pf3D7_07_v3 617933 + 2935 1.165 0.776 1.554 3.264 3.969 3.24e-04 2.92e-02 0.245 mitochondrial ribosomal protein S5 precursor, putative NA
41 PF3D7_0404900 Pf3D7_04_v3 267244 - 1137 1.903 1.310 2.495 3.340 3.976 3.31e-04 2.92e-02 0.231 6-cysteine protein P41
65 PF3D7_0509000 Pf3D7_05_v3 376855 - 1598 -0.641 -1.129 -0.152 5.782 -3.938 3.55e-04 2.94e-02 0.094 SNAP protein (soluble N-ethylmaleimide-sensitive factor attachment protein), putative NA
143 PF3D7_0810800 Pf3D7_08_v3 548200 + 2417 -1.107 -1.926 -0.288 7.387 -3.954 3.49e-04 2.94e-02 0.064 hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase PPPK-DHPS
275 PF3D7_1303000 Pf3D7_13_v3 158144 + 635 -1.133 -2.435 0.170 3.355 -3.939 3.54e-04 2.94e-02 0.170 conserved Plasmodium protein, unknown function NA
139 PF3D7_0805600 Pf3D7_08_v3 312034 + 927 0.774 0.335 1.213 7.188 3.895 4.02e-04 3.22e-02 -0.097 PAP2-like protein, putative NA
315 PF3D7_1400100 Pf3D7_14_v3 1393 + 3951 -1.321 -1.729 -0.913 4.966 -3.901 4.04e-04 3.22e-02 0.021 erythrocyte membrane protein 1 (PfEMP1), pseudogene NA
251 PF3D7_1230500 Pf3D7_12_v3 1253973 - 1509 0.909 -0.278 2.097 4.436 3.879 4.22e-04 3.30e-02 -0.002 WD repeat-containing protein, putative NA
24 PF3D7_0300100 Pf3D7_03_v3 36965 + 7518 -1.134 -1.505 -0.762 4.351 -3.865 4.39e-04 3.32e-02 -0.035 erythrocyte membrane protein 1, PfEMP1 VAR
265 PF3D7_1246600 Pf3D7_12_v3 1936522 + 1173 -0.852 -1.815 0.111 5.347 -3.864 4.40e-04 3.32e-02 -0.078 pre-mRNA-splicing factor CWC26, putative BUD13
7 PF3D7_0113000 Pf3D7_01_v3 487892 - 2236 -1.480 -3.080 0.121 11.345 -3.858 5.27e-04 3.64e-02 -0.387 glutamic acid-rich protein GARP
237 PF3D7_1212800 Pf3D7_12_v3 565966 + 966 1.021 0.421 1.621 2.457 3.805 5.22e-04 3.64e-02 -0.185 iron-sulfur subunit of succinate dehydrogenase NA
260 PF3D7_1240900 Pf3D7_12_v3 1735543 + 7866 -1.406 -2.440 -0.371 4.296 -3.816 5.12e-04 3.64e-02 -0.165 erythrocyte membrane protein 1, PfEMP1 VAR
267 PF3D7_1249000 Pf3D7_12_v3 2005175 - 2019 1.002 0.352 1.652 1.154 3.821 4.98e-04 3.64e-02 -0.189 conserved Plasmodium membrane protein, unknown function NA
347 PF3D7_1457000 Pf3D7_14_v3 2336649 - 2505 -0.648 -1.396 0.101 8.961 -3.813 5.11e-04 3.64e-02 -0.374 signal peptide peptidase SPP
83 PF3D7_0532300 Pf3D7_05_v3 1308278 + 1663 -1.199 -1.939 -0.459 10.800 -3.818 5.46e-04 3.65e-02 -0.417 Plasmodium exported protein (PHISTb), unknown function NA
316 PF3D7_1401400 Pf3D7_14_v3 53411 - 324 -0.853 -1.218 -0.488 12.466 -3.797 5.42e-04 3.65e-02 -0.445 early transcribed membrane protein 14.1 ETRAMP14
111 PF3D7_0704600 Pf3D7_07_v3 216024 - 13049 -0.663 -1.466 0.140 10.228 -3.766 5.84e-04 3.78e-02 -0.524 E3 ubiquitin-protein ligase UT
205 PF3D7_1105300 Pf3D7_11_v3 231847 - 2392 1.352 1.003 1.700 1.696 3.767 5.82e-04 3.78e-02 -0.299 conserved Plasmodium protein, unknown function NA
211 PF3D7_1118400 Pf3D7_11_v3 699869 - 921 1.065 0.445 1.685 3.280 3.756 6.02e-04 3.84e-02 -0.298 haloacid dehalogenase-like hydrolase, putative NA
262 PF3D7_1244200 Pf3D7_12_v3 1852844 - 2838 1.031 0.729 1.333 5.481 3.739 6.32e-04 3.97e-02 -0.420 RNA polymerase II transcription factor B subunit 2, putative TFB2
54 PF3D7_0419800 Pf3D7_04_v3 874811 - 711 0.644 0.109 1.179 5.924 3.733 6.43e-04 3.98e-02 -0.460 60S ribosomal protein L7ae/L30e, putative NA
13 PF3D7_0201900 Pf3D7_02_v3 91318 - 7521 -1.527 -2.211 -0.843 10.614 -3.763 6.87e-04 4.12e-02 -0.612 erythrocyte membrane protein 3 EMP3
146 PF3D7_0821500 Pf3D7_08_v3 967901 - 840 0.820 0.569 1.070 4.918 3.706 6.94e-04 4.12e-02 -0.471 ribosomal RNA small subunit methyltransferase NEP1, putative NEP1
147 PF3D7_0822200 Pf3D7_08_v3 982570 + 5127 1.108 0.550 1.666 2.942 3.700 7.07e-04 4.12e-02 -0.438 conserved Plasmodium membrane protein, unknown function NA
149 PF3D7_0823800 Pf3D7_08_v3 1043813 + 1968 -0.753 -1.486 -0.020 5.245 -3.700 7.05e-04 4.12e-02 -0.518 DnaJ protein, putative NA
51 PF3D7_0417400 Pf3D7_04_v3 756294 + 20310 -0.792 -1.152 -0.432 8.067 -3.685 7.37e-04 4.24e-02 -0.703 conserved Plasmodium protein, unknown function NA
121 PF3D7_0712800 Pf3D7_07_v3 581386 - 7538 -1.348 -2.079 -0.616 4.007 -3.677 7.57e-04 4.24e-02 -0.508 erythrocyte membrane protein 1, PfEMP1 VAR
154 PF3D7_0831700 Pf3D7_08_v3 1365467 - 2040 -0.982 -1.261 -0.702 13.434 -3.690 7.53e-04 4.24e-02 -0.742 heat shock protein 70 HSP70-x
1 mal_rna_11:rRNA M76611 1916 - 108 -1.640 -2.203 -1.077 1.870 -3.641 8.35e-04 4.27e-02 -0.606 NA NA
25 PF3D7_0302800 Pf3D7_03_v3 148046 - 1260 1.163 0.554 1.772 5.270 3.630 8.76e-04 4.27e-02 -0.700 conserved Plasmodium protein, unknown function NA
47 PF3D7_0413900 Pf3D7_04_v3 623168 - 3059 -0.742 -1.627 0.143 6.964 -3.656 8.01e-04 4.27e-02 -0.736 ubiquitin carboxyl-terminal hydrolase 13, putative USP13
57 PF3D7_0423800 Pf3D7_04_v3 1076347 + 1188 2.290 1.835 2.746 2.134 3.628 9.24e-04 4.27e-02 -0.670 cysteine-rich protective antigen CyRPA
68 PF3D7_0512000 Pf3D7_05_v3 527639 + 1028 -1.030 -1.691 -0.369 5.218 -3.609 9.15e-04 4.27e-02 -0.741 prefoldin subunit 6, putative NA
81 PF3D7_0529000 Pf3D7_05_v3 1186787 - 2160 0.470 -0.311 1.252 7.651 3.631 8.60e-04 4.27e-02 -0.831 conserved Plasmodium protein, unknown function NA
103 PF3D7_0629600 Pf3D7_06_v3 1218307 + 945 0.546 0.103 0.988 4.979 3.605 9.25e-04 4.27e-02 -0.734 conserved Plasmodium protein, unknown function NA
116 PF3D7_0711200 Pf3D7_07_v3 495238 + 3003 1.222 0.659 1.785 2.256 3.636 8.47e-04 4.27e-02 -0.603 conserved Plasmodium protein, unknown function NA
132 PF3D7_0733000 Pf3D7_07_v3 1417588 - 8647 -1.043 -1.615 -0.471 4.926 -3.623 8.79e-04 4.27e-02 -0.686 erythrocyte membrane protein 1, PfEMP1 VAR
161 PF3D7_0909600 Pf3D7_09_v3 433238 - 2136 1.511 1.178 1.843 0.836 3.642 8.34e-04 4.27e-02 -0.635 conserved Plasmodium protein, unknown function NA
197 PF3D7_1041300 Pf3D7_10_v3 1642401 - 7548 -1.101 -1.727 -0.474 4.981 -3.628 8.68e-04 4.27e-02 -0.674 erythrocyte membrane protein 1, PfEMP1 VAR
213 PF3D7_1121100 Pf3D7_11_v3 794254 - 5308 -0.793 -1.429 -0.157 8.461 -3.604 9.27e-04 4.27e-02 -0.914 conserved Plasmodium protein, unknown function NA
298 PF3D7_1346200 Pf3D7_13_v3 1845878 - 507 2.002 1.693 2.312 0.978 3.614 9.19e-04 4.27e-02 -0.701 nuclear import protein MOG1, putative NA
326 PF3D7_1421150 Pf3D7_14_v3 875173 - 149 -1.649 -2.239 -1.059 1.022 -3.645 8.26e-04 4.27e-02 -0.626 C/D small nucleolar RNA NA
337 PF3D7_1444800 Pf3D7_14_v3 1844041 - 1577 -0.692 -1.263 -0.122 10.290 -3.622 8.81e-04 4.27e-02 -0.901 fructose-bisphosphate aldolase FBPA
346 PF3D7_1451800 Pf3D7_14_v3 2123461 + 3139 -0.690 -1.189 -0.190 4.615 -3.616 8.96e-04 4.27e-02 -0.702 sortilin NA
207 PF3D7_1108700 Pf3D7_11_v3 373238 - 1623 0.745 0.222 1.267 6.854 3.584 9.81e-04 4.47e-02 -0.904 heat shock protein DnaJ homologue Pfj2 NA
95 PF3D7_0617200 Pf3D7_06_v3 717050 + 1868 -1.064 -2.315 0.188 7.853 -3.587 1.03e-03 4.57e-02 -0.992 conserved Plasmodium protein, unknown function NA
299 PF3D7_1346400 Pf3D7_13_v3 1852898 + 17967 -0.706 -0.963 -0.449 7.849 -3.569 1.02e-03 4.57e-02 -1.005 conserved Plasmodium protein, unknown function NA
259 PF3D7_1240600 Pf3D7_12_v3 1719574 + 7883 -1.224 -1.818 -0.629 3.851 -3.554 1.07e-03 4.66e-02 -0.814 erythrocyte membrane protein 1, PfEMP1 VAR
303 PF3D7_1354300 Pf3D7_13_v3 2164239 - 3178 -0.517 -1.135 0.102 9.432 -3.556 1.06e-03 4.66e-02 -1.078 large subunit rRNA methyltransferase, putative NA
220 PF3D7_1126300 Pf3D7_11_v3 1026976 + 2569 1.067 0.818 1.316 4.596 3.543 1.10e-03 4.76e-02 -0.877 DnaJ protein, putative NA
62 PF3D7_0503100 Pf3D7_05_v3 127064 - 1614 -1.336 -1.742 -0.929 2.177 -3.504 1.23e-03 4.80e-02 -0.920 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, putative IspE
99 PF3D7_0622700 Pf3D7_06_v3 916000 - 1300 1.532 0.053 3.011 1.425 3.534 1.13e-03 4.80e-02 -0.858 conserved Plasmodium membrane protein, unknown function NA
128 PF3D7_0719500 Pf3D7_07_v3 854652 - 2003 0.995 0.204 1.786 1.461 3.509 1.21e-03 4.80e-02 -0.921 LEM3/CDC50 family protein, putative NA
170 PF3D7_0928500 Pf3D7_09_v3 1146239 - 959 -1.164 -2.209 -0.119 2.608 -3.509 1.21e-03 4.80e-02 -0.908 conserved Plasmodium protein, unknown function NA
177 PF3D7_1003900 Pf3D7_10_v3 177921 + 950 1.677 0.884 2.470 0.332 3.524 1.16e-03 4.80e-02 -0.924 conserved Plasmodium protein, unknown function NA
180 PF3D7_1012000 Pf3D7_10_v3 463493 + 3514 -0.679 -1.272 -0.085 6.052 -3.496 1.26e-03 4.80e-02 -1.090 E3 ubiquitin-protein ligase, putative NA
202 PF3D7_1102800 Pf3D7_11_v3 131703 - 285 -0.910 -1.825 0.006 13.470 -3.540 1.15e-03 4.80e-02 -1.138 early transcribed membrane protein 11.2 ETRAMP11.2
288 PF3D7_1321600 Pf3D7_13_v3 897716 + 3329 1.398 0.495 2.301 0.132 3.515 1.19e-03 4.80e-02 -0.956 phosphodiesterase gamma, putative PDEgamma
310 PF3D7_1365600 Pf3D7_13_v3 2621261 + 2740 0.733 -0.151 1.617 4.139 3.495 1.26e-03 4.80e-02 -0.967 DNA topoisomerase VI, b subunit, putative NA
331 PF3D7_1428100 Pf3D7_14_v3 1098038 - 1914 0.966 0.460 1.473 3.882 3.497 1.26e-03 4.80e-02 -0.959 WW domain-binding protein 11, putative NA
341 PF3D7_1446900 Pf3D7_14_v3 1924425 - 2226 0.763 0.448 1.079 6.864 3.500 1.24e-03 4.80e-02 -1.127 glutaminyl-peptide cyclotransferase, putative NA
349 PF3D7_1457900 Pf3D7_14_v3 2375579 + 10368 -0.756 -1.417 -0.094 5.650 -3.528 1.15e-03 4.80e-02 -0.978 conserved Plasmodium protein, unknown function NA
356 PF3D7_1470200 Pf3D7_14_v3 2877586 - 1163 -0.675 -1.356 0.006 5.398 -3.515 1.19e-03 4.80e-02 -0.983 conserved Plasmodium protein, unknown function NA
138 PF3D7_0804900 Pf3D7_08_v3 279711 - 1476 0.919 -0.323 2.160 5.949 3.480 1.32e-03 4.96e-02 -1.116 GTPase-activating protein, putative NA
338 PF3D7_1445600 Pf3D7_14_v3 1871778 + 2604 0.679 0.247 1.112 8.272 3.476 1.33e-03 4.97e-02 -1.260 RNA-binding protein, putative NA
127 PF3D7_0717600 Pf3D7_07_v3 758720 - 4158 -1.473 -1.889 -1.056 3.059 -3.474 1.36e-03 5.02e-02 -1.008 conserved Plasmodium protein, unknown function NA
73 PF3D7_0522300 Pf3D7_05_v3 902613 - 2232 -0.572 -1.174 0.030 6.700 -3.459 1.39e-03 5.09e-02 -1.227 S-adenosylmethionine-dependent methyltransferase, putative NA
343 PF3D7_1449900 Pf3D7_14_v3 2044007 - 1023 1.308 0.758 1.858 2.638 3.457 1.40e-03 5.09e-02 -1.031 conserved Plasmodium protein, unknown function NA
148 PF3D7_0823200 Pf3D7_08_v3 1022629 - 1218 -0.619 -0.974 -0.264 9.617 -3.453 1.42e-03 5.12e-02 -1.351 RNA-binding protein, putative NA
335 PF3D7_1437800 Pf3D7_14_v3 1530276 - 555 1.770 1.086 2.453 2.830 3.457 1.44e-03 5.16e-02 -1.054 trafficking protein particle complex subunit 5, putative TRAPPC5
28 PF3D7_0305000 Pf3D7_03_v3 234058 - 1277 0.947 0.074 1.820 3.438 3.441 1.47e-03 5.16e-02 -1.086 elongation factor Ts EF-Ts
209 PF3D7_1111300 Pf3D7_11_v3 442959 - 870 0.841 0.548 1.135 2.945 3.438 1.48e-03 5.16e-02 -1.079 SNARE protein, putative GS27
305 PF3D7_1355700 Pf3D7_13_v3 2206592 - 3867 1.237 0.365 2.109 7.278 3.465 1.48e-03 5.16e-02 -1.296 NLI interacting factor-like phosphatase, putative NIF3
19 PF3D7_0216000 Pf3D7_02_v3 658636 + 5994 -2.074 -2.621 -1.528 0.535 -3.431 1.53e-03 5.29e-02 -1.141 DEAD/DEAH box helicase, putative NA
53 PF3D7_0419500 Pf3D7_04_v3 866501 - 1611 1.223 0.163 2.283 3.890 3.421 1.55e-03 5.30e-02 -1.144 conserved Plasmodium membrane protein, unknown function NA
114 PF3D7_0708500 Pf3D7_07_v3 385583 - 2739 -0.737 -1.370 -0.105 6.652 -3.415 1.58e-03 5.35e-02 -1.337 heat shock protein 86 family protein NA
69 PF3D7_0513600 Pf3D7_05_v3 574941 - 3565 -1.045 -1.363 -0.726 5.614 -3.413 1.61e-03 5.39e-02 -1.283 deoxyribodipyrimidine photo-lyase, putative NA
210 PF3D7_1115200 Pf3D7_11_v3 576773 + 3504 -0.659 -1.554 0.236 8.247 -3.404 1.63e-03 5.39e-02 -1.445 histone-lysine N-methyltransferase SET7 SET7
229 PF3D7_1145500 Pf3D7_11_v3 1807359 + 2772 1.102 0.252 1.951 1.564 3.404 1.63e-03 5.39e-02 -1.163 ABC transporter B family member 3, putative ABCB3
59 PF3D7_0501300 Pf3D7_05_v3 68930 + 1184 -0.925 -1.601 -0.250 12.486 -3.399 1.71e-03 5.59e-02 -1.517 skeleton-binding protein 1 SBP1
246 PF3D7_1225600 Pf3D7_12_v3 1035261 - 2895 -0.478 -2.453 1.498 8.007 -3.386 1.71e-03 5.59e-02 -1.485 conserved Plasmodium protein, unknown function NA
324 PF3D7_1417600 Pf3D7_14_v3 730694 - 13989 -0.568 -1.358 0.222 8.915 -3.382 1.73e-03 5.59e-02 -1.523 conserved Plasmodium protein, unknown function NA
297 PF3D7_1345200 Pf3D7_13_v3 1812220 - 1710 1.084 0.716 1.452 3.402 3.379 1.74e-03 5.59e-02 -1.227 rhomboid protease ROM6, putative ROM6
29 PF3D7_0310800 Pf3D7_03_v3 464662 + 330 0.487 -0.214 1.187 6.132 3.360 1.84e-03 5.68e-02 -1.439 conserved Plasmodium protein, unknown function NA
122 PF3D7_0712900 Pf3D7_07_v3 590326 - 7408 -1.100 -1.332 -0.869 4.206 -3.367 1.80e-03 5.68e-02 -1.294 erythrocyte membrane protein 1, PfEMP1 VAR
190 PF3D7_1025000 Pf3D7_10_v3 1045608 - 4153 -0.570 -0.985 -0.156 8.252 -3.366 1.80e-03 5.68e-02 -1.534 formin 2, putative NA
212 PF3D7_1119200 Pf3D7_11_v3 722717 - 573 -1.038 -1.443 -0.632 3.783 -3.361 1.83e-03 5.68e-02 -1.279 conserved protein, unknown function NA
218 PF3D7_1124800 Pf3D7_11_v3 976880 - 1057 -0.568 -1.158 0.023 6.670 -3.363 1.82e-03 5.68e-02 -1.469 nuclear preribosomal assembly protein, putative NA
234 PF3D7_1206300 Pf3D7_12_v3 281020 - 8283 -1.407 -1.752 -1.062 1.456 -3.354 1.87e-03 5.73e-02 -1.280 conserved Plasmodium protein, unknown function NA
50 PF3D7_0416100 Pf3D7_04_v3 706529 + 2481 -0.909 -1.422 -0.396 4.248 -3.345 1.91e-03 5.78e-02 -1.360 glutamyl-tRNA(Gln) amidotransferase subunit A GATA
106 PF3D7_0700100 Pf3D7_07_v3 20307 + 7777 -1.044 -1.871 -0.217 5.158 -3.344 1.93e-03 5.78e-02 -1.411 erythrocyte membrane protein 1, PfEMP1 VAR
203 PF3D7_1103400 Pf3D7_11_v3 146427 + 4389 1.198 -0.028 2.425 3.263 3.343 1.93e-03 5.78e-02 -1.310 FeS cluster assembly protein SufD, putative SufD
42 PF3D7_0405400 Pf3D7_04_v3 291251 + 9726 -0.562 -1.533 0.410 10.748 -3.333 1.97e-03 5.87e-02 -1.665 pre-mRNA-processing-splicing factor 8, putative PRPF8
56 PF3D7_0421300 Pf3D7_04_v3 969031 - 7561 -1.056 -1.582 -0.531 4.877 -3.320 2.05e-03 5.87e-02 -1.447 erythrocyte membrane protein 1, PfEMP1 VAR
247 PF3D7_1226600 Pf3D7_12_v3 1077868 - 909 1.498 0.096 2.900 -0.283 3.319 2.05e-03 5.87e-02 -1.406 proliferating cell nuclear antigen 2 PCNA2
255 PF3D7_1234500 Pf3D7_12_v3 1439896 - 1155 0.626 0.114 1.138 4.918 3.325 2.02e-03 5.87e-02 -1.435 conserved Plasmodium protein, unknown function NA
308 PF3D7_1364000 Pf3D7_13_v3 2564625 + 2484 0.987 0.420 1.554 3.797 3.328 2.01e-03 5.87e-02 -1.369 conserved Plasmodium protein, unknown function NA
313 PF3D7_1372100 Pf3D7_13_v3 2837053 + 2006 3.129 2.299 3.958 1.578 3.365 2.06e-03 5.87e-02 -1.336 Plasmodium exported protein (PHISTb), unknown function GEXP04
339 PF3D7_1445800 Pf3D7_14_v3 1878658 - 3920 1.067 0.776 1.358 1.539 3.321 2.05e-03 5.87e-02 -1.355 conserved Plasmodium membrane protein, unknown function NA
280 PF3D7_1307700 Pf3D7_13_v3 344525 + 3708 0.582 -0.368 1.531 6.383 3.313 2.09e-03 5.94e-02 -1.581 conserved Plasmodium protein, unknown function NA
109 PF3D7_0703400 Pf3D7_07_v3 129370 - 2463 1.161 0.838 1.484 3.395 3.307 2.12e-03 5.99e-02 -1.406 conserved Plasmodium protein, unknown function NA
183 PF3D7_1016100 Pf3D7_10_v3 643558 - 774 1.160 0.663 1.658 0.683 3.303 2.15e-03 6.01e-02 -1.409 conserved Plasmodium protein, unknown function NA
358 PF3D7_1477700 Pf3D7_14_v3 3202931 + 1087 2.091 1.317 2.865 1.770 3.316 2.17e-03 6.04e-02 -1.395 Plasmodium exported protein (PHISTa), unknown function Pfg14-748
64 PF3D7_0508700 Pf3D7_05_v3 358261 + 4473 -0.499 -1.326 0.327 7.639 -3.287 2.24e-03 6.05e-02 -1.721 pre-mRNA-processing ATP-dependent RNA helicase PRP5, putative PRP5
144 PF3D7_0814100 Pf3D7_08_v3 682518 - 1055 0.938 -0.783 2.659 4.348 3.287 2.24e-03 6.05e-02 -1.492 conserved Plasmodium protein, unknown function NA
178 PF3D7_1009300 Pf3D7_10_v3 377906 - 1803 1.211 0.885 1.536 3.019 3.287 2.24e-03 6.05e-02 -1.441 conserved Plasmodium protein, unknown function NA
295 PF3D7_1344200 Pf3D7_13_v3 1769129 + 2799 -0.564 -1.236 0.108 9.434 -3.286 2.25e-03 6.05e-02 -1.777 heat shock protein 110, putative HSP110
330 PF3D7_1427200 Pf3D7_14_v3 1061805 + 975 -1.619 -2.155 -1.082 1.505 -3.289 2.25e-03 6.05e-02 -1.430 selenoprotein Sel4
44 PF3D7_0412400 Pf3D7_04_v3 545987 - 7824 -0.919 -1.577 -0.261 3.465 -3.283 2.27e-03 6.06e-02 -1.458 erythrocyte membrane protein 1, PfEMP1 VAR
32 PF3D7_0317100 Pf3D7_03_v3 686282 + 3201 0.874 0.596 1.152 2.504 3.274 2.33e-03 6.06e-02 -1.464 6-cysteine protein B9
82 PF3D7_0531000 Pf3D7_05_v3 1267410 + 2130 0.713 -0.601 2.027 4.964 3.276 2.31e-03 6.06e-02 -1.559 conserved Plasmodium protein, unknown function NA
134 PF3D7_0800300 Pf3D7_08_v3 40948 + 9992 -1.073 -1.392 -0.753 5.027 -3.282 2.29e-03 6.06e-02 -1.553 erythrocyte membrane protein 1, PfEMP1 VAR
289 PF3D7_1321700 Pf3D7_13_v3 902383 + 2784 -0.538 -0.896 -0.181 9.122 -3.276 2.31e-03 6.06e-02 -1.799 splicing factor 1 SF1
273 PF3D7_1302700 Pf3D7_13_v3 145174 + 5025 -0.474 -1.190 0.241 8.882 -3.270 2.35e-03 6.09e-02 -1.808 ATP-dependent RNA helicase DHR1, putative NA
169 PF3D7_0926500 Pf3D7_09_v3 1075915 - 5769 1.173 0.733 1.614 0.469 3.256 2.44e-03 6.26e-02 -1.518 conserved Plasmodium protein, unknown function NA
221 PF3D7_1128100 Pf3D7_11_v3 1094909 - 1023 -0.703 -1.004 -0.402 5.252 -3.253 2.46e-03 6.26e-02 -1.636 prefoldin subunit 5, putative NA
233 PF3D7_1205700 Pf3D7_12_v3 253155 + 969 1.229 0.775 1.684 0.855 3.254 2.45e-03 6.26e-02 -1.515 targeted glyoxalase II tGloII
17 PF3D7_0209700 Pf3D7_02_v3 400153 - 1707 0.555 -0.119 1.228 8.789 3.232 2.61e-03 6.32e-02 -1.899 RING zinc finger protein, putative NA
22 PF3D7_0220500 Pf3D7_02_v3 823825 - 1040 -0.875 -2.077 0.327 6.458 -3.238 2.57e-03 6.32e-02 -1.757 Plasmodium exported protein (hyp2), unknown function NA
87 PF3D7_0606800 Pf3D7_06_v3 288377 - 900 1.551 1.311 1.791 3.382 3.241 2.60e-03 6.32e-02 -1.573 probable protein, unknown function NA
130 PF3D7_0723900 Pf3D7_07_v3 1000701 - 4046 -0.612 -0.899 -0.325 7.826 -3.238 2.57e-03 6.32e-02 -1.851 RNA-binding protein, putative NA
187 PF3D7_1021900 Pf3D7_10_v3 905473 - 6873 -0.993 -1.349 -0.638 6.736 -3.246 2.57e-03 6.32e-02 -1.784 PHAX domain-containing protein, putative NA
199 PF3D7_1100300 Pf3D7_11_v3 45056 + 1178 1.993 1.575 2.412 -0.537 3.236 2.60e-03 6.32e-02 -1.598 rifin RIF
241 PF3D7_1217000 Pf3D7_12_v3 674349 - 429 1.119 0.313 1.924 1.672 3.236 2.58e-03 6.32e-02 -1.546 conserved Plasmodium protein, unknown function NA
317 PF3D7_1401600 Pf3D7_14_v3 61364 - 1625 -0.760 -1.042 -0.478 8.852 -3.236 2.61e-03 6.32e-02 -1.901 Plasmodium exported protein (PHISTb), unknown function NA
70 PF3D7_0518300 Pf3D7_05_v3 759831 - 1168 -0.484 -0.912 -0.056 6.571 -3.226 2.65e-03 6.33e-02 -1.809 proteasome subunit beta type-1, putative NA
72 PF3D7_0521000 Pf3D7_05_v3 859373 - 1691 -0.687 -1.390 0.017 5.971 -3.225 2.66e-03 6.33e-02 -1.762 conserved Plasmodium protein, unknown function NA
98 PF3D7_0621500 Pf3D7_06_v3 881963 + 1032 1.065 0.072 2.058 1.161 3.225 2.65e-03 6.33e-02 -1.574 ribonuclease P/MRP protein subunit RPP1, putative RPP1
174 PF3D7_0936800 Pf3D7_09_v3 1458392 + 1471 -0.876 -1.190 -0.562 10.878 -3.220 2.77e-03 6.48e-02 -1.957 Plasmodium exported protein (PHISTc), unknown function NA
181 PF3D7_1013000 Pf3D7_10_v3 500210 + 2012 1.140 0.529 1.751 2.844 3.208 2.78e-03 6.48e-02 -1.624 zinc finger protein, putative NA
184 PF3D7_1016200 Pf3D7_10_v3 646054 + 1683 1.055 0.321 1.789 4.570 3.206 2.80e-03 6.48e-02 -1.710 Rab3 GTPase-activating protein non-catalytic subunit, putative NA
227 PF3D7_1140800 Pf3D7_11_v3 1633920 + 2412 0.505 -0.045 1.055 6.676 3.212 2.75e-03 6.48e-02 -1.849 conserved Plasmodium protein, unknown function NA
230 PF3D7_1149500 Pf3D7_11_v3 1991359 - 2660 -0.653 -1.498 0.192 8.007 -3.204 2.81e-03 6.48e-02 -1.927 ring-infected erythrocyte surface antigen 2, pseudogene RESA2
319 PF3D7_1410500 Pf3D7_14_v3 423751 - 500 1.042 0.705 1.378 1.400 3.205 2.80e-03 6.48e-02 -1.618 conserved Plasmodium protein, unknown function NA
104 PF3D7_0631600 Pf3D7_06_v3 1323294 + 1142 -1.234 -1.641 -0.828 2.559 -3.201 2.83e-03 6.49e-02 -1.631 exported protein family 4 EPF4
323 PF3D7_1414500 Pf3D7_14_v3 578369 - 9161 -0.636 -0.920 -0.351 7.984 -3.197 2.86e-03 6.52e-02 -1.965 atypical protein kinase, ABC-1 family, putative ABCk2
12 PF3D7_0201800 Pf3D7_02_v3 86832 - 1960 -0.527 -0.803 -0.252 9.437 -3.178 3.02e-03 6.61e-02 -2.046 knob associated heat shock protein 40 KAHsp40
33 PF3D7_0317500 Pf3D7_03_v3 716523 - 5309 0.587 -0.080 1.253 7.115 3.180 3.00e-03 6.61e-02 -1.961 kinesin-5 EG5
52 PF3D7_0418300 Pf3D7_04_v3 819362 - 2979 0.610 0.114 1.106 10.470 3.186 2.95e-03 6.61e-02 -2.036 conserved Plasmodium protein, unknown function NA
67 PF3D7_0511000 Pf3D7_05_v3 467585 - 516 -0.538 -0.738 -0.337 8.120 -3.185 2.96e-03 6.61e-02 -1.988 translationally-controlled tumor protein homolog TCTP
263 PF3D7_1244300 Pf3D7_12_v3 1857849 + 242 -1.945 -2.961 -0.930 2.568 -3.199 2.97e-03 6.61e-02 -1.662 ACEA small nucleolar RNA U3 NA
277 PF3D7_1304300 Pf3D7_13_v3 231083 + 642 1.477 0.660 2.294 0.552 3.180 3.00e-03 6.61e-02 -1.683 conserved Plasmodium protein, unknown function NA
278 PF3D7_1305400 Pf3D7_13_v3 268785 - 1953 0.561 0.218 0.904 5.309 3.182 2.98e-03 6.61e-02 -1.821 AAR2 protein, putative NA
34 PF3D7_0319600 Pf3D7_03_v3 817913 + 783 -0.442 -0.957 0.073 8.336 -3.170 3.08e-03 6.72e-02 -2.045 elongation factor 1 (EF-1), putative NA
195 PF3D7_1035800 Pf3D7_10_v3 1420533 + 2139 -1.293 -1.677 -0.909 9.469 -3.201 3.10e-03 6.72e-02 -2.007 probable protein, unknown function M712
283 PF3D7_1309400 Pf3D7_13_v3 431892 + 3984 -0.750 -1.414 -0.086 5.757 -3.166 3.12e-03 6.72e-02 -1.885 HORMA domain protein, putative NA
173 PF3D7_0935900 Pf3D7_09_v3 1420483 - 2325 -0.762 -1.083 -0.440 13.744 -3.169 3.13e-03 6.73e-02 -2.072 ring-exported protein 1 REX1
152 PF3D7_0829100 Pf3D7_08_v3 1252349 + 1448 -0.521 -1.286 0.244 7.060 -3.160 3.16e-03 6.75e-02 -2.006 conserved protein, unknown function NA
222 PF3D7_1133000 Pf3D7_11_v3 1275574 + 90 1.310 0.942 1.678 0.955 3.158 3.18e-03 6.77e-02 -1.727 conserved Plasmodium protein, unknown function NA
16 PF3D7_0205400 Pf3D7_02_v3 223478 + 1374 0.446 0.105 0.787 6.179 3.149 3.26e-03 6.80e-02 -1.969 PCI domain-containing protein, putative NA
55 PF3D7_0420000 Pf3D7_04_v3 894612 - 10113 -0.524 -1.375 0.327 9.311 -3.146 3.29e-03 6.80e-02 -2.125 zinc finger protein, putative NA
182 PF3D7_1015800 Pf3D7_10_v3 633682 + 1605 1.197 0.525 1.870 0.318 3.151 3.24e-03 6.80e-02 -1.749 ribonucleoside-diphosphate reductase small chain, putative NA
258 PF3D7_1240400 Pf3D7_12_v3 1704512 + 7979 -0.936 -1.157 -0.715 4.827 -3.148 3.27e-03 6.80e-02 -1.857 erythrocyte membrane protein 1, PfEMP1 VAR
355 PF3D7_1468100 Pf3D7_14_v3 2786308 - 8016 -0.558 -0.954 -0.161 10.206 -3.146 3.28e-03 6.80e-02 -2.133 conserved Plasmodium protein, unknown function NA
357 PF3D7_1472300 Pf3D7_14_v3 2954108 + 3001 1.050 0.167 1.932 4.451 3.145 3.30e-03 6.80e-02 -1.843 conserved Plasmodium membrane protein, unknown function NA
66 PF3D7_0509800 Pf3D7_05_v3 410268 + 5041 -0.385 -0.757 -0.013 8.254 -3.141 3.33e-03 6.80e-02 -2.114 phosphatidylinositol 4-kinase PI4K
232 PF3D7_1200200 Pf3D7_12_v3 26321 - 1367 -1.845 -2.273 -1.417 -0.252 -3.141 3.33e-03 6.80e-02 -1.797 rifin RIF
226 PF3D7_1140200 Pf3D7_11_v3 1601257 - 1822 -1.160 -1.579 -0.742 3.820 -3.140 3.35e-03 6.81e-02 -1.826 conserved Plasmodium protein, unknown function NA
348 PF3D7_1457100 Pf3D7_14_v3 2340784 + 2244 -0.895 -1.549 -0.240 6.629 -3.139 3.39e-03 6.85e-02 -2.013 conserved Plasmodium protein, unknown function NA
200 PF3D7_1102600 Pf3D7_11_v3 123818 - 919 1.461 0.883 2.039 2.317 3.132 3.43e-03 6.91e-02 -1.791 Plasmodium exported protein, unknown function GEXP14
112 PF3D7_0705600 Pf3D7_07_v3 281035 - 3399 0.833 0.363 1.303 3.988 3.125 3.48e-03 6.96e-02 -1.857 RNA helicase, putative NA
352 PF3D7_1460500 Pf3D7_14_v3 2466091 + 4899 1.016 0.429 1.604 2.431 3.123 3.49e-03 6.96e-02 -1.807 conserved Plasmodium protein, unknown function NA
3 PF3D7_0101000 Pf3D7_01_v3 65817 - 1173 -2.246 -2.928 -1.565 -1.073 -3.119 3.57e-03 7.06e-02 -1.882 rifin RIF
90 PF3D7_0609700 Pf3D7_06_v3 413652 + 6130 -0.563 -1.557 0.430 9.552 -3.111 3.61e-03 7.06e-02 -2.211 conserved Plasmodium protein, unknown function NA
186 PF3D7_1019300 Pf3D7_10_v3 774929 - 5559 0.842 0.580 1.103 4.369 3.114 3.58e-03 7.06e-02 -1.903 zinc finger protein, putative NA
272 PF3D7_1301400 Pf3D7_13_v3 82718 + 1301 -0.891 -1.162 -0.619 8.053 -3.118 3.61e-03 7.06e-02 -2.129 Plasmodium exported protein (hyp12), unknown function HYP12
165 PF3D7_0915500 Pf3D7_09_v3 657418 + 1995 1.320 0.789 1.851 0.044 3.109 3.63e-03 7.07e-02 -1.847 conserved Plasmodium protein, unknown function NA
123 PF3D7_0713500 Pf3D7_07_v3 614385 + 2865 0.925 0.534 1.316 4.314 3.100 3.72e-03 7.07e-02 -1.938 conserved Plasmodium protein, unknown function NA
141 PF3D7_0808700 Pf3D7_08_v3 440408 + 7655 -0.981 -1.345 -0.618 4.547 -3.102 3.69e-03 7.07e-02 -1.952 erythrocyte membrane protein 1, PfEMP1 VAR
145 PF3D7_0817100 Pf3D7_08_v3 774299 + 2493 1.043 0.215 1.870 0.070 3.101 3.70e-03 7.07e-02 -1.864 tRNA modification GTPase, putative NA
162 PF3D7_0913100 Pf3D7_09_v3 571031 - 2319 1.169 0.432 1.905 -0.164 3.102 3.69e-03 7.07e-02 -1.865 conserved Plasmodium protein, unknown function NA
345 PF3D7_1451100 Pf3D7_14_v3 2090902 + 2499 -0.648 -1.295 -0.001 12.559 -3.105 3.67e-03 7.07e-02 -2.231 elongation factor 2 eEF2
281 PF3D7_1308300 Pf3D7_13_v3 372260 + 387 0.444 -0.083 0.971 7.958 3.092 3.80e-03 7.19e-02 -2.222 40S ribosomal protein S27 RPS27
27 PF3D7_0304900 Pf3D7_03_v3 231793 - 513 0.801 0.116 1.486 5.085 3.080 3.92e-03 7.22e-02 -2.035 conserved Plasmodium protein, unknown function NA
76 PF3D7_0524800 Pf3D7_05_v3 1021408 - 2900 0.882 0.028 1.736 3.247 3.087 3.84e-03 7.22e-02 -1.915 ubiquitin fusion degradation protein 1, putative UFD1
225 PF3D7_1137300 Pf3D7_11_v3 1466197 - 2070 0.450 -0.267 1.166 7.350 3.080 3.92e-03 7.22e-02 -2.218 CLPTM1 domain-containing protein, putative NA
252 PF3D7_1231600 Pf3D7_12_v3 1301098 - 3507 -0.706 -1.747 0.336 6.288 -3.084 3.88e-03 7.22e-02 -2.140 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP2, putative PRP2
282 PF3D7_1309100 Pf3D7_13_v3 418820 + 1302 -0.722 -1.280 -0.165 8.832 -3.088 3.87e-03 7.22e-02 -2.267 60S ribosomal protein L24, putative NA
291 PF3D7_1324200 Pf3D7_13_v3 1000100 - 1783 -0.797 -1.141 -0.454 7.145 -3.086 3.89e-03 7.22e-02 -2.192 micro-fibrillar-associated protein, putative NA
119 PF3D7_0712300 Pf3D7_07_v3 542906 - 7615 -1.223 -2.264 -0.181 3.752 -3.079 3.97e-03 7.25e-02 -1.970 erythrocyte membrane protein 1, PfEMP1 VAR
307 PF3D7_1362300 Pf3D7_13_v3 2493143 + 570 0.782 -0.312 1.876 3.668 3.075 3.97e-03 7.25e-02 -1.960 conserved protein, unknown function NA
240 PF3D7_1215900 Pf3D7_12_v3 641552 + 1968 0.743 0.298 1.187 4.806 3.068 4.04e-03 7.35e-02 -2.053 serpentine receptor, putative SR10
20 PF3D7_0216400 Pf3D7_02_v3 675431 + 2169 0.789 0.122 1.457 0.530 3.064 4.09e-03 7.37e-02 -1.935 vacuolar protein sorting-associated protein 45, putative VPS45
172 PF3D7_0932900 Pf3D7_09_v3 1309467 - 477 0.939 0.530 1.349 2.103 3.065 4.08e-03 7.37e-02 -1.934 conserved Plasmodium protein, unknown function NA
292 PF3D7_1326700 Pf3D7_13_v3 1125280 + 1629 1.336 0.904 1.768 3.634 3.063 4.16e-03 7.46e-02 -1.997 conserved Apicomplexan protein, unknown function NA
160 PF3D7_0907900 Pf3D7_09_v3 367865 - 925 -1.480 -2.225 -0.735 3.656 -3.067 4.19e-03 7.48e-02 -2.006 peptide deformylase PDF
333 PF3D7_1434300 Pf3D7_14_v3 1372903 + 1695 -0.408 -1.424 0.608 8.746 -3.050 4.25e-03 7.55e-02 -2.352 Hsp70/Hsp90 organizing protein HOP
353 PF3D7_1462800 Pf3D7_14_v3 2559098 + 1250 -0.693 -1.932 0.546 13.081 -3.050 4.27e-03 7.56e-02 -2.364 glyceraldehyde-3-phosphate dehydrogenase GAPDH
5 PF3D7_0108500 Pf3D7_01_v3 349170 + 540 -0.875 -2.335 0.586 10.163 -3.051 4.39e-03 7.58e-02 -2.381 conserved Plasmodium protein, unknown function NA
10 PF3D7_0200100 Pf3D7_02_v3 25232 + 5937 -1.299 -2.059 -0.540 3.963 -3.049 4.33e-03 7.58e-02 -2.044 erythrocyte membrane protein 1, PfEMP1 VAR
214 PF3D7_1122300 Pf3D7_11_v3 846929 + 1086 0.944 0.421 1.466 3.809 3.043 4.32e-03 7.58e-02 -2.047 conserved Plasmodium protein, unknown function NA
215 PF3D7_1122900 Pf3D7_11_v3 878969 + 16305 -1.086 -1.508 -0.664 1.411 -3.039 4.37e-03 7.58e-02 -1.988 dynein heavy chain, putative NA
254 PF3D7_1233100 Pf3D7_12_v3 1359169 + 408 -0.794 -1.469 -0.119 4.068 -3.041 4.35e-03 7.58e-02 -2.051 conserved protein, unknown function NA
270 PF3D7_1253100 Pf3D7_12_v3 2171342 + 1008 0.614 0.151 1.077 6.992 3.039 4.37e-03 7.58e-02 -2.295 Plasmodium exported protein (PHISTa), unknown function NA
115 PF3D7_0709600 Pf3D7_07_v3 429857 - 3902 -0.489 -0.848 -0.129 7.337 -3.035 4.41e-03 7.59e-02 -2.325 ribonucleases P/MRP protein subunit POP1, putative POP1
223 PF3D7_1133700 Pf3D7_11_v3 1302173 + 3815 -0.680 -1.110 -0.249 10.033 -3.034 4.46e-03 7.60e-02 -2.412 FHA domain-containing protein, putative NA
264 PF3D7_1244800 Pf3D7_12_v3 1873194 - 2094 -0.452 -2.303 1.399 7.567 -3.030 4.48e-03 7.60e-02 -2.356 cytoplasmic translation machinery associated protein, putative NA
269 PF3D7_1251400 Pf3D7_12_v3 2097436 - 1410 1.035 0.691 1.379 1.657 3.031 4.46e-03 7.60e-02 -2.004 conserved Plasmodium protein, unknown function NA
48 PF3D7_0415300 Pf3D7_04_v3 681810 + 4159 -0.547 -0.925 -0.169 8.627 -3.020 4.59e-03 7.68e-02 -2.419 cdc2-related protein kinase 3 CRK3
108 PF3D7_0703200 Pf3D7_07_v3 122513 - 4623 -0.955 -1.527 -0.383 4.508 -3.017 4.63e-03 7.68e-02 -2.153 conserved Plasmodium protein, unknown function NA
118 PF3D7_0712000 Pf3D7_07_v3 527338 - 7794 -1.572 -1.966 -1.178 3.236 -3.029 4.61e-03 7.68e-02 -2.059 erythrocyte membrane protein 1, PfEMP1 VAR
155 PF3D7_0833500 Pf3D7_08_v3 1435794 - 7656 -0.978 -1.408 -0.547 4.340 -3.022 4.57e-03 7.68e-02 -2.123 erythrocyte membrane protein 1, PfEMP1 VAR
188 PF3D7_1023000 Pf3D7_10_v3 961066 - 1242 0.838 0.065 1.610 1.337 3.016 4.65e-03 7.68e-02 -2.035 conserved Plasmodium membrane protein, unknown function NA
300 PF3D7_1347500 Pf3D7_13_v3 1897983 - 1380 -0.472 -0.748 -0.196 12.054 -3.015 4.65e-03 7.68e-02 -2.454 DNA/RNA-binding protein Alba 4 ALBA4
318 PF3D7_1404900 Pf3D7_14_v3 170000 + 894 0.405 -0.046 0.855 8.338 3.020 4.59e-03 7.68e-02 -2.410 conserved Plasmodium protein, unknown function NA
92 PF3D7_0613600 Pf3D7_06_v3 554457 + 3772 1.236 0.284 2.188 0.053 3.009 4.73e-03 7.71e-02 -2.056 conserved Plasmodium protein, unknown function NA
125 PF3D7_0716000 Pf3D7_07_v3 703207 + 3378 -0.490 -0.849 -0.130 8.568 -3.008 4.74e-03 7.71e-02 -2.448 RNA-binding protein, putative NA
167 PF3D7_0923100 Pf3D7_09_v3 941830 - 669 1.113 0.506 1.720 1.302 3.009 4.73e-03 7.71e-02 -2.049 OTU domain-containing protein, putative NA
239 PF3D7_1214600 Pf3D7_12_v3 613561 - 1014 -0.563 -1.043 -0.084 4.766 -3.012 4.70e-03 7.71e-02 -2.178 adrenodoxin-type ferredoxin, putative NA
100 PF3D7_0625400 Pf3D7_06_v3 1032536 - 1239 0.554 -0.780 1.888 7.778 3.005 4.77e-03 7.73e-02 -2.416 conserved Plasmodium protein, unknown function NA
79 PF3D7_0528100 Pf3D7_05_v3 1157840 - 3714 -0.377 -1.096 0.342 9.370 -2.997 4.88e-03 7.81e-02 -2.490 AP-1 complex subunit beta, putative NA
191 PF3D7_1025500 Pf3D7_10_v3 1067652 - 19341 -1.108 -1.901 -0.316 0.450 -2.998 4.86e-03 7.81e-02 -2.074 conserved Plasmodium protein, unknown function NA
194 PF3D7_1030100 Pf3D7_10_v3 1224519 - 4574 -0.406 -1.677 0.865 8.759 -2.997 4.88e-03 7.81e-02 -2.478 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22, putative PRP22
77 PF3D7_0527500 Pf3D7_05_v3 1143618 + 1742 -0.398 -1.848 1.052 9.586 -2.992 4.94e-03 7.83e-02 -2.505 Hsc70-interacting protein HIP
131 PF3D7_0724000 Pf3D7_07_v3 1006335 + 5811 0.875 0.418 1.332 2.241 2.994 4.92e-03 7.83e-02 -2.094 Rab GTPase activator and protein kinase, putative NA
268 PF3D7_1250800 Pf3D7_12_v3 2077718 + 5170 -0.475 -0.773 -0.177 6.852 -2.991 4.95e-03 7.83e-02 -2.402 DNA repair protein rhp16, putative NA
340 PF3D7_1446300 Pf3D7_14_v3 1898351 + 3576 1.129 0.535 1.724 4.066 2.990 5.01e-03 7.90e-02 -2.191 conserved Plasmodium membrane protein, unknown function NA
179 PF3D7_1011800 Pf3D7_10_v3 455398 + 3420 -0.579 -1.305 0.146 10.624 -2.984 5.04e-03 7.92e-02 -2.531 PRE-binding protein PREBP
274 PF3D7_1302900 Pf3D7_13_v3 154992 + 2403 1.025 0.147 1.903 3.537 2.980 5.10e-03 7.98e-02 -2.176 conserved Plasmodium protein, unknown function NA
235 PF3D7_1208600 Pf3D7_12_v3 402300 + 228 -0.700 -1.229 -0.171 3.757 -2.977 5.15e-03 8.00e-02 -2.206 mitochondrial import inner membrane translocase subunit TIM10, putative TIM10
284 PF3D7_1309600 Pf3D7_13_v3 438510 + 867 0.727 0.325 1.129 4.309 2.976 5.15e-03 8.00e-02 -2.227 ribosomal RNA methyltransferase, putative NA
11 PF3D7_0201600 Pf3D7_02_v3 77251 - 1558 -0.649 -1.469 0.172 9.150 -2.971 5.23e-03 8.01e-02 -2.534 PHISTb domain-containing RESA-like protein 1 RLP1
18 PF3D7_0211800 Pf3D7_02_v3 475242 + 1833 -0.643 -1.218 -0.068 9.283 -2.961 5.37e-03 8.01e-02 -2.576 asparagine–tRNA ligase AsnRS
97 PF3D7_0621300 Pf3D7_06_v3 873809 + 2382 0.443 -0.422 1.307 7.592 2.960 5.37e-03 8.01e-02 -2.519 mRNA binding Pumilio-homology domain protein, putative NA
129 PF3D7_0719900 Pf3D7_07_v3 865927 + 10206 -0.417 -1.081 0.248 7.724 -2.959 5.39e-03 8.01e-02 -2.534 conserved Plasmodium membrane protein, unknown function NA
135 PF3D7_0801700 Pf3D7_08_v3 112299 + 5579 -0.589 -0.932 -0.246 6.129 -2.966 5.29e-03 8.01e-02 -2.408 sentrin-specific protease 2, putative SENP2
137 PF3D7_0804700 Pf3D7_08_v3 271417 - 5997 -0.573 -1.463 0.317 5.755 -2.962 5.34e-03 8.01e-02 -2.382 conserved Plasmodium protein, unknown function NA
159 PF3D7_0907700 Pf3D7_09_v3 364069 - 840 0.415 0.186 0.645 7.929 2.970 5.23e-03 8.01e-02 -2.513 subunit of proteaseome activator complex, putative PA28
217 PF3D7_1124100 Pf3D7_11_v3 951382 - 4962 -0.411 -0.946 0.123 8.014 -2.963 5.34e-03 8.01e-02 -2.538 beige/BEACH domain protein, putative NA
256 PF3D7_1235300 Pf3D7_12_v3 1470713 + 4989 -0.568 -1.359 0.222 9.292 -2.966 5.29e-03 8.01e-02 -2.560 CCR4-NOT transcription complex subunit 4, putative NOT4
301 PF3D7_1350100 Pf3D7_13_v3 2005962 - 1989 -0.430 -1.427 0.567 9.206 -2.962 5.34e-03 8.01e-02 -2.572 lysine–tRNA ligase KRS1
312 PF3D7_1366500 Pf3D7_13_v3 2661573 + 450 1.090 0.675 1.506 0.730 2.968 5.26e-03 8.01e-02 -2.136 nucleoside diphosphate kinase NDK
350 PF3D7_1458000 Pf3D7_14_v3 2387786 + 1710 0.339 -0.118 0.796 8.196 2.974 5.19e-03 8.01e-02 -2.513 cysteine proteinase falcipain 1 FP1
61 PF3D7_0502500 Pf3D7_05_v3 114149 + 1785 1.611 0.861 2.360 0.201 2.957 5.42e-03 8.02e-02 -2.162 conserved Plasmodium protein, unknown function NA
354 PF3D7_1466300 Pf3D7_14_v3 2709418 + 3775 -0.392 -1.138 0.353 9.366 -2.954 5.46e-03 8.05e-02 -2.594 26S proteasome regulatory subunit RPN2, putative RPN2
151 PF3D7_0826900 Pf3D7_08_v3 1164655 + 2551 0.987 0.185 1.788 3.078 2.949 5.54e-03 8.14e-02 -2.215 conserved Plasmodium protein, unknown function NA
80 PF3D7_0528800 Pf3D7_05_v3 1180425 - 1614 0.476 -0.329 1.281 6.073 2.942 5.64e-03 8.23e-02 -2.454 nucleolar preribosomal GTPase, putative NA
257 PF3D7_1239800 Pf3D7_12_v3 1660451 + 17304 -1.106 -1.531 -0.682 3.686 -2.944 5.62e-03 8.23e-02 -2.275 conserved Plasmodium protein, unknown function NA
39 PF3D7_0404300 Pf3D7_04_v3 234014 - 3000 -0.853 -1.708 0.001 7.533 -2.947 5.68e-03 8.23e-02 -2.559 conserved Plasmodium protein, unknown function NA
185 PF3D7_1019100 Pf3D7_10_v3 766168 - 5787 -1.392 -1.726 -1.058 0.749 -2.939 5.67e-03 8.23e-02 -2.197 conserved Plasmodium protein, unknown function NA
304 PF3D7_1355200 Pf3D7_13_v3 2191058 - 3054 1.630 0.890 2.370 0.536 2.939 5.71e-03 8.24e-02 -2.201 RAP protein, putative NA
328 PF3D7_1424500 Pf3D7_14_v3 979464 + 142 -0.825 -1.714 0.063 3.590 -2.929 5.82e-03 8.37e-02 -2.272 small nucleolar RNA snoR27 NA
293 PF3D7_1338600 Pf3D7_13_v3 1556659 - 3076 1.267 0.697 1.837 0.039 2.928 5.85e-03 8.39e-02 -2.223 conserved Plasmodium protein, unknown function NA
311 PF3D7_1366000 Pf3D7_13_v3 2635213 + 276 1.117 0.785 1.450 2.202 2.924 5.91e-03 8.45e-02 -2.247 conserved Plasmodium protein, unknown function NA
236 PF3D7_1210300 Pf3D7_12_v3 465115 + 630 0.713 -0.071 1.498 3.554 2.919 5.97e-03 8.51e-02 -2.309 conserved Plasmodium protein, unknown function NA
249 PF3D7_1228900 Pf3D7_12_v3 1180670 - 4814 -0.607 -1.072 -0.142 6.434 -2.916 6.03e-03 8.56e-02 -2.550 conserved Plasmodium protein, unknown function NA
8 PF3D7_0115200 Pf3D7_01_v3 591849 + 1339 -2.053 -3.146 -0.961 -0.691 -2.917 6.08e-03 8.59e-02 -2.271 rifin RIF
30 PF3D7_0311700 Pf3D7_03_v3 502698 + 3151 -1.459 -2.316 -0.601 0.983 -2.910 6.12e-03 8.59e-02 -2.258 plasmepsin VI NA
46 PF3D7_0412900 Pf3D7_04_v3 576810 - 7859 -1.189 -1.516 -0.862 2.611 -2.911 6.10e-03 8.59e-02 -2.283 erythrocyte membrane protein 1, PfEMP1 VAR
43 PF3D7_0411900 Pf3D7_04_v3 528192 - 6294 -0.914 -1.287 -0.541 1.934 -2.905 6.20e-03 8.62e-02 -2.287 DNA polymerase alpha catalytic subunit A NA
201 PF3D7_1102700 Pf3D7_11_v3 128789 + 276 -0.587 -0.982 -0.192 10.475 -2.905 6.20e-03 8.62e-02 -2.719 early transcribed membrane protein 11.1 ETRAMP11.1
279 PF3D7_1306400 Pf3D7_13_v3 297178 - 1182 -0.466 -1.327 0.396 7.247 -2.904 6.22e-03 8.62e-02 -2.626 26S protease regulatory subunit 10B, putative RPT4
302 PF3D7_1353500 Pf3D7_13_v3 2144125 + 981 0.778 0.133 1.423 3.030 2.907 6.17e-03 8.62e-02 -2.313 RNA polymerase II transcription factor B subunit 4, putative TFB4
2 mal_rna_17:rRNA M76611 5577 - 195 -1.264 -1.671 -0.857 4.223 -2.903 6.33e-03 8.72e-02 -2.371 NA NA
196 PF3D7_1037900 Pf3D7_10_v3 1502955 - 1368 1.025 0.342 1.708 2.136 2.897 6.34e-03 8.72e-02 -2.307 conserved Plasmodium protein, unknown function NA
164 PF3D7_0915100 Pf3D7_09_v3 643232 - 812 -0.531 -1.152 0.090 6.543 -2.889 6.46e-03 8.87e-02 -2.619 SUMO-conjugating enzyme UBC9 UBC9
35 PF3D7_0323000 Pf3D7_03_v3 968675 - 528 -0.901 -1.197 -0.604 4.269 -2.885 6.53e-03 8.91e-02 -2.456 translation machinery-associated protein 7, putative TMA7
309 PF3D7_1365000 Pf3D7_13_v3 2608698 + 1047 -0.839 -1.102 -0.577 3.815 -2.886 6.52e-03 8.91e-02 -2.386 conserved Plasmodium protein, unknown function NA
60 PF3D7_0501400 Pf3D7_05_v3 74509 + 5334 -1.045 -1.303 -0.787 10.998 -2.901 6.65e-03 8.95e-02 -2.757 interspersed repeat antigen FIRA
75 PF3D7_0523700 Pf3D7_05_v3 980754 - 4601 1.308 0.350 2.266 0.920 2.876 6.69e-03 8.95e-02 -2.331 conserved Plasmodium membrane protein, unknown function NA
86 PF3D7_0601600 Pf3D7_06_v3 68833 - 861 1.227 -0.183 2.636 1.035 2.873 6.74e-03 8.95e-02 -2.337 tetratricopeptide repeat protein, putative NA
93 PF3D7_0613900 Pf3D7_06_v3 579435 - 6462 1.190 -0.386 2.767 0.943 2.874 6.72e-03 8.95e-02 -2.334 myosin E, putative myoE
96 PF3D7_0618200 Pf3D7_06_v3 764667 - 826 -0.533 -1.152 0.086 7.015 -2.871 6.78e-03 8.95e-02 -2.700 conserved Plasmodium protein, unknown function NA
101 PF3D7_0625600 Pf3D7_06_v3 1039655 + 1896 0.840 -0.298 1.979 5.615 2.878 6.67e-03 8.95e-02 -2.563 poly(A) polymerase PAP, putative NA
163 PF3D7_0913200 Pf3D7_09_v3 575679 + 831 -0.503 -1.221 0.215 8.866 -2.871 6.77e-03 8.95e-02 -2.781 elongation factor 1-beta EF-1beta
228 PF3D7_1142400 Pf3D7_11_v3 1702089 - 1554 0.593 -0.547 1.732 5.970 2.878 6.64e-03 8.95e-02 -2.601 coproporphyrinogen-III oxidase CPO
276 PF3D7_1303100 Pf3D7_13_v3 159024 + 892 -0.764 -1.043 -0.485 3.651 -2.879 6.62e-03 8.95e-02 -2.429 methyltransferase-like protein, putative NA
334 PF3D7_1436500 Pf3D7_14_v3 1488706 + 1296 1.054 0.135 1.972 0.183 2.873 6.73e-03 8.95e-02 -2.335 GTP-binding protein, putative NA
110 PF3D7_0703700 Pf3D7_07_v3 146645 - 750 0.495 -0.380 1.370 7.579 2.868 6.82e-03 8.98e-02 -2.733 conserved Plasmodium protein, unknown function NA
171 PF3D7_0931400 Pf3D7_09_v3 1263347 + 1484 -0.845 -1.123 -0.567 3.547 -2.862 6.93e-03 9.00e-02 -2.430 conserved Plasmodium protein, unknown function NA
206 PF3D7_1108600 Pf3D7_11_v3 369675 - 1032 -0.677 -1.052 -0.302 9.227 -2.866 6.92e-03 9.00e-02 -2.795 endoplasmic reticulum-resident calcium binding protein ERC
306 PF3D7_1360100 Pf3D7_13_v3 2405249 - 969 -0.524 -0.778 -0.270 5.582 -2.864 6.88e-03 9.00e-02 -2.583 RNA-binding protein, putative NA
329 PF3D7_1426000 Pf3D7_14_v3 1016133 - 486 0.490 0.116 0.864 8.627 2.863 6.90e-03 9.00e-02 -2.789 60S ribosomal protein L21 RPL21
15 PF3D7_0202500 Pf3D7_02_v3 127994 + 321 -0.663 -1.051 -0.275 12.139 -2.862 6.99e-03 9.04e-02 -2.822 early transcribed membrane protein 2 ETRAMP2
157 PF3D7_0903100 Pf3D7_09_v3 130140 - 798 0.695 0.070 1.319 4.700 2.858 7.00e-03 9.04e-02 -2.523 protein RER1, putative RER1
21 PF3D7_0218700 Pf3D7_02_v3 763491 - 1701 -0.606 -1.170 -0.042 7.123 -2.852 7.11e-03 9.05e-02 -2.738 pre-mRNA-processing protein 45, putative PRP45
150 PF3D7_0826100 Pf3D7_08_v3 1113369 - 25776 -0.526 -0.989 -0.064 10.275 -2.853 7.08e-03 9.05e-02 -2.840 E3 ubiquitin-protein ligase, putative NA
192 PF3D7_1027300 Pf3D7_10_v3 1140589 - 2014 -0.763 -1.045 -0.481 8.469 -2.857 7.12e-03 9.05e-02 -2.799 peroxiredoxin nPrx
250 PF3D7_1229600 Pf3D7_12_v3 1214043 - 3673 -1.015 -1.610 -0.421 1.452 -2.855 7.06e-03 9.05e-02 -2.378 conserved Plasmodium protein, unknown function NA
266 PF3D7_1247400 Pf3D7_12_v3 1955124 - 915 -0.628 -1.393 0.137 6.237 -2.853 7.10e-03 9.05e-02 -2.676 peptidyl-prolyl cis-trans isomerase FKBP35 FKBP35
78 PF3D7_0528000 Pf3D7_05_v3 1156205 - 375 0.784 -1.169 2.738 3.675 2.849 7.17e-03 9.08e-02 -2.472 proteasome maturation factor UMP1, putative UMP1
91 PF3D7_0612700 Pf3D7_06_v3 525987 - 1044 0.819 -0.189 1.826 1.993 2.847 7.20e-03 9.08e-02 -2.405 6-cysteine protein P12
325 PF3D7_1417700 Pf3D7_14_v3 750330 + 1355 -0.593 -0.956 -0.231 4.828 -2.846 7.21e-03 9.08e-02 -2.565 conserved Plasmodium protein, unknown function NA
49 PF3D7_0416000 Pf3D7_04_v3 701526 - 2637 -0.691 -1.273 -0.108 6.293 -2.845 7.24e-03 9.09e-02 -2.698 RNA-binding protein, putative NA
26 PF3D7_0303400 Pf3D7_03_v3 178420 + 2708 1.000 0.628 1.372 1.354 2.833 7.46e-03 9.26e-02 -2.423 palmitoyltransferase DHHC1 DHHC1
158 PF3D7_0905300 Pf3D7_09_v3 251353 - 18357 -0.896 -1.244 -0.548 2.709 -2.834 7.44e-03 9.26e-02 -2.466 dynein heavy chain, putative NA
208 PF3D7_1111000 Pf3D7_11_v3 434802 + 1740 0.564 -0.224 1.352 5.391 2.833 7.46e-03 9.26e-02 -2.644 tRNA m5C-methyltransferase, putative NA
327 PF3D7_1423200 Pf3D7_14_v3 933059 + 2299 -0.588 -0.881 -0.294 5.853 -2.834 7.45e-03 9.26e-02 -2.693 peptidyl-prolyl cis-trans isomerase CYP52
74 PF3D7_0523300 Pf3D7_05_v3 970266 - 697 1.001 0.197 1.805 0.700 2.826 7.59e-03 9.29e-02 -2.431 conserved Plasmodium protein, unknown function NA
176 PF3D7_1002300 Pf3D7_10_v3 117242 + 1293 0.867 0.028 1.706 1.347 2.827 7.58e-03 9.29e-02 -2.437 conserved Plasmodium protein, unknown function NA
290 PF3D7_1322100 Pf3D7_13_v3 920971 + 8479 -0.528 -1.188 0.132 9.385 -2.826 7.59e-03 9.29e-02 -2.884 histone-lysine N-methyltransferase SET2 SET2
294 PF3D7_1341100 Pf3D7_13_v3 1632602 - 108 -1.102 -1.788 -0.415 3.017 -2.826 7.60e-03 9.29e-02 -2.477 U6 spliceosomal RNA NA
314 PF3D7_1373500 Pf3D7_13_v3 2884786 - 7555 -0.781 -1.245 -0.318 4.450 -2.826 7.60e-03 9.29e-02 -2.573 erythrocyte membrane protein 1, PfEMP1 VAR
245 PF3D7_1225200 Pf3D7_12_v3 1024455 - 3564 0.382 -0.352 1.116 6.893 2.824 7.64e-03 9.32e-02 -2.796 conserved Plasmodium protein, unknown function NA
63 PF3D7_0506700 Pf3D7_05_v3 280886 + 2460 -0.562 -1.252 0.128 4.982 -2.815 7.81e-03 9.49e-02 -2.662 GTPase-activating protein, putative NA
219 PF3D7_1126100 Pf3D7_11_v3 1018366 - 4130 0.858 0.339 1.377 1.600 2.811 7.90e-03 9.57e-02 -2.475 autophagy-related protein 7, putative ATG7
88 PF3D7_0607000 Pf3D7_06_v3 293864 + 2934 -0.447 -1.635 0.742 10.481 -2.807 7.97e-03 9.61e-02 -2.949 translation initiation factor IF-2, putative NA
94 PF3D7_0614200 Pf3D7_06_v3 593172 - 2733 0.813 -0.615 2.241 3.914 2.807 7.98e-03 9.61e-02 -2.582 cytosolic Fe-S cluster assembly factor NAR1, putative NAR1
140 PF3D7_0808600 Pf3D7_08_v3 431165 + 7887 -0.842 -1.341 -0.344 4.353 -2.804 8.04e-03 9.66e-02 -2.623 erythrocyte membrane protein 1, PfEMP1 VAR
126 PF3D7_0717400 Pf3D7_07_v3 751877 + 2256 -0.411 -1.105 0.283 7.621 -2.802 8.08e-03 9.67e-02 -2.889 queuine tRNA-ribosyltransferase, putative NA
332 PF3D7_1431600 Pf3D7_14_v3 1244018 + 1389 1.118 0.219 2.016 1.156 2.798 8.15e-03 9.74e-02 -2.493 succinyl-CoA ligase [ADP-forming] subunit beta, putative NA
38 PF3D7_0400200 Pf3D7_04_v3 38955 + 1200 -1.094 -1.337 -0.852 2.992 -2.789 8.34e-03 9.86e-02 -2.562 erythrocyte membrane protein 1 (PfEMP1), exon 2, pseudogene NA
89 PF3D7_0608700 Pf3D7_06_v3 358391 + 1813 -0.362 -0.916 0.193 9.108 -2.789 8.35e-03 9.86e-02 -2.977 T-complex protein 1 subunit zeta CCT6
344 PF3D7_1450300 Pf3D7_14_v3 2056641 + 2598 0.766 0.095 1.436 5.175 2.789 8.35e-03 9.86e-02 -2.742 NADPH–cytochrome P450 reductase, putative CPR
351 PF3D7_1459300 Pf3D7_14_v3 2432177 + 570 0.803 0.428 1.178 1.803 2.789 8.35e-03 9.86e-02 -2.529 OPA3-like protein, putative NA
320 PF3D7_1412700 Pf3D7_14_v3 512363 + 3660 -0.569 -1.258 0.119 5.935 -2.787 8.40e-03 9.89e-02 -2.800 AAA family ATPase, putative NA
113 PF3D7_0707900 Pf3D7_07_v3 366929 + 780 -0.414 -1.143 0.315 7.553 -2.784 8.46e-03 9.90e-02 -2.928 ribosomal protein S8e, putative NA
261 PF3D7_1244100 Pf3D7_12_v3 1847677 + 4480 -0.482 -0.753 -0.210 5.912 -2.781 8.53e-03 9.90e-02 -2.816 N-alpha-acetyltransferase 15, NatA auxiliary subunit, putative NA
321 PF3D7_1414100 Pf3D7_14_v3 560093 + 2232 0.548 -0.272 1.368 6.992 2.781 8.51e-03 9.90e-02 -2.898 conserved Plasmodium protein, unknown function NA
336 PF3D7_1439100 Pf3D7_14_v3 1580750 + 8108 -0.574 -0.972 -0.177 6.512 -2.782 8.50e-03 9.90e-02 -2.863 DEAD/DEAH box helicase, putative NA
342 PF3D7_1447200 Pf3D7_14_v3 1933985 + 1791 -0.429 -0.856 -0.001 7.819 -2.781 8.52e-03 9.90e-02 -2.951 conserved Plasmodium protein, unknown function NA
253 PF3D7_1232200 Pf3D7_12_v3 1333134 + 1763 -0.941 -1.961 0.079 0.865 -2.777 8.60e-03 9.95e-02 -2.534 dihydrolipoyl dehydrogenase, mitochondrial LPD1

Heatmap of deregulated genes

col_annot <- data.frame(row.names = colnames(v$E), stringsAsFactors = F)
col_annot$phenotype[substring(colnames(v$E), 1, 1) == "I"] <- "non-severe"
col_annot$phenotype[substring(colnames(v$E), 1, 1) == "S"] <- "severe"
col_annot$phenotype <- as.factor(col_annot$phenotype)

pheatmap(v2$E[rownames(v$E) %in% top_ring_ruv$GeneID, ], show_rownames = FALSE, scale = "row", annotation_col = col_annot, annotation_colors = list(phenotype = c(`non-severe` = colors[1], 
    severe = colors[2])))

Gene set analysis

First GO set enrichment using limma’s mroast.

# genesets <- AnnotationDbi::select(org.Pf.plasmo.db, keys=top_ring_ruv$GeneID, keytype='ALIAS', columns = c('GO','PATH')) go.gene.sets <-
# lapply(split.data.frame(genesets,genesets$GO), function(x) as.vector(x$ALIAS)) kegg.gene.sets <- lapply(split.data.frame(genesets,genesets$PATH),
# function(x) as.vector(x$ALIAS))
MIN_SET_SIZE <- 3

go.gene.df <- fread("./data/go_gene_lists.txt", sep = "\t", data.table = FALSE)
go.gene.sets <- lapply(go.gene.df$Genes, function(x) {
    x <- unlist(str_split(x, ","))
    x <- x[x != ""]
})
names(go.gene.sets) <- go.gene.df$GO_ID
go.gene.sets <- go.gene.sets[unlist(lapply(go.gene.sets, length)) >= MIN_SET_SIZE]

kegg.gene.df <- fread("./data/kegg_gene_lists.txt", sep = "\t", data.table = FALSE)
kegg.gene.sets <- lapply(kegg.gene.df$Genes, function(x) {
    x <- unlist(str_split(x, ","))
    x <- x[x != ""]
})
names(kegg.gene.sets) <- kegg.gene.df$KEGG_ID
kegg.gene.sets <- kegg.gene.sets[unlist(lapply(kegg.gene.sets, length)) >= MIN_SET_SIZE]

indices <- ids2indices(go.gene.sets, rownames(v2), remove.empty = TRUE)
go_mr <- mroast(v2, index = indices, design = modRUV, contrast = 2, nrot = 10000, set.statistic = "floormean")
go_cam <- camera(v2, index = indices, design = modRUV, contrast = 2)

go_mr$PValue <- format(go_mr$PValue, scientific = TRUE, digits = 3)
go_mr$FDR <- format(go_mr$FDR, scientific = TRUE, digits = 3)
go_mr$PValue.Mixed <- format(go_mr$PValue.Mixed, scientific = TRUE, digits = 3)
go_mr$FDR.Mixed <- format(go_mr$FDR.Mixed, scientific = TRUE, digits = 3)
kable(go_mr, digits = 3)
NGenes PropDown PropUp Direction PValue FDR PValue.Mixed FDR.Mixed
GO:0016337 54 0.852 0.019 Down 1.00e-04 1.46e-03 1.00e-04 1.34e-03
GO:0098602 54 0.852 0.019 Down 1.00e-04 1.46e-03 1.00e-04 1.34e-03
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GO:0044093 4 0.250 0.250 Down 2.80e-01 3.22e-01 6.40e-02 8.55e-02
GO:0009123 18 0.111 0.278 Up 2.82e-01 3.23e-01 8.71e-02 1.09e-01
GO:0019692 3 0.333 0.000 Down 2.82e-01 3.23e-01 1.18e-01 1.43e-01
GO:0043952 5 0.200 0.200 Down 2.85e-01 3.26e-01 2.81e-02 4.77e-02
GO:0009200 3 0.333 0.000 Down 2.86e-01 3.27e-01 1.21e-01 1.45e-01
GO:0043085 4 0.250 0.250 Down 2.87e-01 3.27e-01 6.79e-02 8.93e-02
GO:0009394 3 0.333 0.000 Down 2.87e-01 3.27e-01 1.23e-01 1.47e-01
GO:0007264 24 0.167 0.125 Down 2.90e-01 3.30e-01 4.05e-02 5.98e-02
GO:0006370 3 0.000 0.000 Down 2.92e-01 3.32e-01 3.04e-01 3.34e-01
GO:0009069 7 0.000 0.286 Up 2.93e-01 3.33e-01 2.41e-01 2.70e-01
GO:1901292 20 0.150 0.150 Down 2.94e-01 3.34e-01 5.38e-02 7.37e-02
GO:0009161 18 0.111 0.278 Up 2.95e-01 3.34e-01 9.50e-02 1.17e-01
GO:0040029 3 0.333 0.000 Down 3.03e-01 3.43e-01 2.83e-01 3.14e-01
GO:0006429 2 0.500 0.000 Down 3.06e-01 3.46e-01 2.00e-01 2.31e-01
GO:0006360 3 0.333 0.000 Down 3.07e-01 3.47e-01 8.80e-02 1.10e-01
GO:0006720 7 0.143 0.143 Down 3.11e-01 3.51e-01 3.57e-02 5.50e-02
GO:0007067 11 0.000 0.091 Up 3.11e-01 3.51e-01 5.29e-01 5.50e-01
GO:0008299 7 0.143 0.143 Down 3.15e-01 3.54e-01 3.73e-02 5.68e-02
GO:0016458 3 0.333 0.333 Down 3.15e-01 3.55e-01 4.13e-02 6.03e-02
GO:0006040 4 0.250 0.250 Up 3.18e-01 3.58e-01 9.36e-02 1.16e-01
GO:0016925 4 0.250 0.250 Down 3.22e-01 3.62e-01 4.59e-02 6.47e-02
GO:0006269 2 0.000 0.500 Up 3.25e-01 3.64e-01 2.89e-01 3.20e-01
GO:0006072 5 0.400 0.200 Down 3.27e-01 3.66e-01 1.10e-01 1.35e-01
GO:0052646 6 0.333 0.333 Up 3.29e-01 3.68e-01 4.37e-02 6.24e-02
GO:0007169 3 0.000 0.000 Up 3.44e-01 3.84e-01 4.87e-01 5.12e-01
GO:0006302 5 0.000 0.200 Up 3.47e-01 3.88e-01 3.28e-01 3.59e-01
GO:0007167 3 0.000 0.000 Up 3.51e-01 3.91e-01 4.88e-01 5.12e-01
GO:1901071 3 0.333 0.333 Down 3.55e-01 3.95e-01 1.27e-01 1.52e-01
GO:0009190 3 0.333 0.000 Down 3.55e-01 3.95e-01 2.37e-01 2.67e-01
GO:0051168 8 0.125 0.125 Down 3.64e-01 4.04e-01 2.30e-01 2.60e-01
GO:0000027 8 0.125 0.000 Down 3.65e-01 4.05e-01 2.92e-01 3.22e-01
GO:0006119 3 0.333 0.333 Down 3.72e-01 4.12e-01 1.30e-01 1.55e-01
GO:0002377 3 0.000 0.000 Up 3.77e-01 4.17e-01 2.12e-01 2.42e-01
GO:0002440 3 0.000 0.000 Up 3.77e-01 4.17e-01 2.09e-01 2.40e-01
GO:0070925 15 0.133 0.067 Down 3.80e-01 4.19e-01 2.93e-01 3.23e-01
GO:0042773 3 0.333 0.333 Down 3.81e-01 4.20e-01 1.28e-01 1.52e-01
GO:0009070 2 0.000 0.500 Up 3.82e-01 4.21e-01 2.22e-01 2.52e-01
GO:0009187 4 0.250 0.000 Down 3.90e-01 4.29e-01 3.80e-01 4.08e-01
GO:0008645 2 0.000 0.000 Up 3.91e-01 4.30e-01 5.05e-01 5.30e-01
GO:0015749 2 0.000 0.000 Up 3.94e-01 4.32e-01 5.13e-01 5.37e-01
GO:0006268 2 0.500 0.000 Down 3.95e-01 4.33e-01 3.39e-01 3.68e-01
GO:0006270 11 0.091 0.182 Up 3.96e-01 4.34e-01 1.86e-01 2.16e-01
GO:0009066 4 0.250 0.000 Down 3.97e-01 4.35e-01 6.64e-01 6.76e-01
GO:0009084 3 0.000 0.000 Down 3.99e-01 4.36e-01 5.27e-01 5.49e-01
GO:0006611 3 0.000 0.333 Up 4.12e-01 4.50e-01 1.83e-01 2.13e-01
GO:0006122 2 0.000 0.500 Up 4.13e-01 4.51e-01 3.52e-01 3.81e-01
GO:0042775 2 0.000 0.500 Up 4.17e-01 4.54e-01 3.51e-01 3.81e-01
GO:0006614 5 0.200 0.200 Down 4.33e-01 4.71e-01 9.28e-02 1.15e-01
GO:0006613 5 0.200 0.200 Down 4.36e-01 4.74e-01 9.49e-02 1.17e-01
GO:0030048 4 0.250 0.250 Up 4.37e-01 4.74e-01 8.63e-02 1.08e-01
GO:0050793 4 0.000 0.250 Up 4.38e-01 4.75e-01 2.79e-01 3.10e-01
GO:0046777 1 0.000 0.000 Up 4.40e-01 4.76e-01 4.40e-01 4.65e-01
GO:0000302 3 0.000 0.000 Up 4.40e-01 4.76e-01 5.27e-01 5.49e-01
GO:1901700 3 0.000 0.000 Up 4.41e-01 4.77e-01 5.28e-01 5.49e-01
GO:0006546 3 0.000 0.333 Up 4.44e-01 4.79e-01 3.92e-01 4.19e-01
GO:0010035 3 0.000 0.000 Up 4.45e-01 4.79e-01 5.26e-01 5.49e-01
GO:0009234 2 0.000 0.000 Up 4.45e-01 4.79e-01 4.21e-01 4.47e-01
GO:0007033 4 0.250 0.000 Down 4.45e-01 4.79e-01 1.27e-01 1.51e-01
GO:0006541 2 0.000 0.000 Down 4.46e-01 4.79e-01 4.22e-01 4.47e-01
GO:0009233 2 0.000 0.000 Up 4.49e-01 4.82e-01 4.28e-01 4.53e-01
GO:0006888 20 0.150 0.150 Down 4.50e-01 4.82e-01 7.38e-02 9.48e-02
GO:0009071 3 0.000 0.333 Up 4.53e-01 4.85e-01 3.95e-01 4.21e-01
GO:0006424 3 0.000 0.000 Up 4.59e-01 4.91e-01 2.71e-01 3.02e-01
GO:0009219 2 0.000 0.000 Up 4.62e-01 4.94e-01 4.64e-01 4.90e-01
GO:0006787 2 0.000 0.000 Down 4.67e-01 4.98e-01 5.06e-01 5.30e-01
GO:0097428 1 0.000 0.000 Down 4.69e-01 5.00e-01 4.69e-01 4.94e-01
GO:0048856 4 0.000 0.250 Up 4.76e-01 5.07e-01 3.66e-01 3.95e-01
GO:0006885 8 0.125 0.125 Down 4.77e-01 5.08e-01 1.56e-01 1.84e-01
GO:0033015 2 0.000 0.000 Down 4.78e-01 5.08e-01 5.16e-01 5.39e-01
GO:0055067 8 0.125 0.125 Down 4.89e-01 5.19e-01 1.58e-01 1.86e-01
GO:0016197 3 0.000 0.000 Down 4.97e-01 5.27e-01 4.03e-01 4.28e-01
GO:0006891 3 0.000 0.000 Up 4.98e-01 5.27e-01 3.96e-01 4.22e-01
GO:0042147 3 0.000 0.000 Down 5.04e-01 5.34e-01 4.01e-01 4.27e-01
GO:0000280 14 0.071 0.071 Up 5.05e-01 5.34e-01 3.36e-01 3.66e-01
GO:0048285 14 0.071 0.071 Up 5.14e-01 5.43e-01 3.41e-01 3.70e-01
GO:0015908 3 0.333 0.000 Up 5.19e-01 5.48e-01 2.69e-01 3.01e-01
GO:0000290 3 0.000 0.000 Down 5.34e-01 5.63e-01 6.44e-01 6.61e-01
GO:0000288 3 0.000 0.000 Down 5.35e-01 5.63e-01 6.48e-01 6.63e-01
GO:0006308 4 0.250 0.000 Up 5.51e-01 5.79e-01 1.77e-01 2.06e-01
GO:0000724 2 0.000 0.000 Down 5.65e-01 5.93e-01 5.40e-01 5.59e-01
GO:0000725 2 0.000 0.000 Down 5.71e-01 5.99e-01 5.43e-01 5.61e-01
GO:0042255 11 0.091 0.091 Down 5.80e-01 6.08e-01 3.27e-01 3.58e-01
GO:0008283 3 0.000 0.000 Up 5.81e-01 6.09e-01 4.72e-01 4.97e-01
GO:0000070 2 0.000 0.000 Down 5.99e-01 6.26e-01 7.90e-01 7.99e-01
GO:0000387 4 0.250 0.000 Down 6.00e-01 6.27e-01 6.00e-01 6.18e-01
GO:0000819 2 0.000 0.000 Down 6.18e-01 6.44e-01 8.04e-01 8.11e-01
GO:0022603 2 0.000 0.000 Up 6.19e-01 6.45e-01 3.95e-01 4.21e-01
GO:0051452 7 0.000 0.143 Up 6.45e-01 6.71e-01 3.24e-01 3.56e-01
GO:0045851 7 0.000 0.143 Up 6.47e-01 6.72e-01 3.25e-01 3.56e-01
GO:0030641 7 0.000 0.143 Up 6.50e-01 6.75e-01 3.32e-01 3.62e-01
GO:0030004 7 0.000 0.143 Up 6.50e-01 6.75e-01 3.30e-01 3.61e-01
GO:0051453 7 0.000 0.143 Up 6.53e-01 6.77e-01 3.36e-01 3.66e-01
GO:0007035 7 0.000 0.143 Up 6.55e-01 6.79e-01 3.27e-01 3.58e-01
GO:0022900 7 0.143 0.143 Up 6.80e-01 7.03e-01 3.88e-01 4.15e-01
GO:0022904 6 0.167 0.167 Up 6.82e-01 7.04e-01 2.79e-01 3.10e-01
GO:0006865 4 0.000 0.000 Up 6.82e-01 7.04e-01 6.48e-01 6.63e-01
GO:0009225 4 0.000 0.000 Up 6.93e-01 7.14e-01 4.49e-01 4.74e-01
GO:0034637 3 0.000 0.000 Down 7.05e-01 7.24e-01 6.05e-01 6.22e-01
GO:0019673 3 0.000 0.000 Down 7.05e-01 7.24e-01 6.06e-01 6.22e-01
GO:0016114 2 0.000 0.000 Down 7.06e-01 7.24e-01 6.45e-01 6.62e-01
GO:0000304 2 0.000 0.000 Up 7.06e-01 7.24e-01 6.51e-01 6.65e-01
GO:0009072 3 0.000 0.000 Up 7.07e-01 7.24e-01 8.02e-01 8.10e-01
GO:0009073 3 0.000 0.000 Up 7.07e-01 7.24e-01 8.03e-01 8.11e-01
GO:0006721 2 0.000 0.000 Down 7.13e-01 7.29e-01 6.49e-01 6.63e-01
GO:0006836 1 0.000 0.000 Down 7.18e-01 7.34e-01 6.62e-01 6.76e-01
GO:0051187 3 0.000 0.000 Down 7.37e-01 7.53e-01 4.78e-01 5.03e-01
GO:0051170 10 0.100 0.000 Down 7.45e-01 7.60e-01 5.42e-01 5.61e-01
GO:0044744 10 0.100 0.000 Down 7.47e-01 7.60e-01 5.37e-01 5.57e-01
GO:0034504 10 0.100 0.000 Down 7.47e-01 7.60e-01 5.43e-01 5.61e-01
GO:1902593 10 0.100 0.000 Down 7.48e-01 7.60e-01 5.38e-01 5.57e-01
GO:0006606 10 0.100 0.000 Down 7.49e-01 7.61e-01 5.45e-01 5.62e-01
GO:0000096 3 0.000 0.000 Down 7.68e-01 7.79e-01 5.29e-01 5.50e-01
GO:0060249 3 0.000 0.000 Down 7.91e-01 8.02e-01 8.30e-01 8.36e-01
GO:0000723 3 0.000 0.000 Down 7.99e-01 8.08e-01 8.33e-01 8.37e-01
GO:0032200 3 0.000 0.000 Down 8.00e-01 8.08e-01 8.33e-01 8.37e-01
GO:0006471 3 0.000 0.000 Up 8.00e-01 8.08e-01 8.34e-01 8.37e-01
GO:0031109 3 0.000 0.000 Up 8.03e-01 8.09e-01 7.11e-01 7.21e-01
GO:0007020 3 0.000 0.000 Up 8.03e-01 8.09e-01 7.14e-01 7.23e-01
GO:0046785 3 0.000 0.000 Up 8.07e-01 8.13e-01 7.15e-01 7.23e-01
GO:0009067 3 0.000 0.000 Down 8.64e-01 8.69e-01 9.18e-01 9.18e-01
GO:0042819 3 0.000 0.000 Up 8.77e-01 8.81e-01 6.96e-01 7.08e-01
GO:0042816 3 0.000 0.000 Up 8.82e-01 8.86e-01 6.95e-01 7.08e-01
GO:0008614 3 0.000 0.000 Up 8.83e-01 8.86e-01 6.98e-01 7.09e-01
GO:0009432 2 0.000 0.000 Down 9.21e-01 9.22e-01 8.52e-01 8.53e-01
GO:0072525 4 0.000 0.000 Down 9.21e-01 9.22e-01 8.34e-01 8.37e-01
GO:0006607 3 0.000 0.000 Down 9.26e-01 9.26e-01 8.40e-01 8.42e-01

Also test using limma’s camera

go_cam$PValue <- format(go_cam$PValue, scientific = TRUE, digits = 3)
go_cam$FDR <- format(go_cam$FDR, scientific = TRUE, digits = 3)
kable(go_cam)
NGenes Direction PValue FDR
GO:0016337 54 Down 9.71e-23 4.68e-20
GO:0098602 54 Down 9.71e-23 4.68e-20
GO:0007155 69 Down 1.93e-18 6.21e-16
GO:0009405 84 Down 6.74e-18 1.62e-15
GO:0020035 93 Down 5.91e-17 5.67e-15
GO:0044406 93 Down 5.91e-17 5.67e-15
GO:0034118 87 Down 9.47e-17 5.67e-15
GO:0020013 87 Down 9.47e-17 5.67e-15
GO:0030155 87 Down 9.47e-17 5.67e-15
GO:0034110 87 Down 9.47e-17 5.67e-15
GO:0022407 87 Down 9.47e-17 5.67e-15
GO:0009607 94 Down 1.15e-16 5.67e-15
GO:0051807 93 Down 1.18e-16 5.67e-15
GO:0051834 93 Down 1.18e-16 5.67e-15
GO:0051832 93 Down 1.18e-16 5.67e-15
GO:0043207 93 Down 1.18e-16 5.67e-15
GO:0051707 93 Down 1.18e-16 5.67e-15
GO:0052173 93 Down 1.18e-16 5.67e-15
GO:0052564 93 Down 1.18e-16 5.67e-15
GO:0051805 93 Down 1.18e-16 5.67e-15
GO:0044068 88 Down 1.50e-16 6.88e-15
GO:0051809 92 Down 1.74e-16 7.29e-15
GO:0020033 92 Down 1.74e-16 7.29e-15
GO:0044003 89 Down 3.52e-16 1.36e-14
GO:0051817 89 Down 3.52e-16 1.36e-14
GO:0009605 100 Down 7.96e-16 2.95e-14
GO:0035821 90 Down 1.27e-15 4.55e-14
GO:0022610 113 Down 1.99e-14 6.86e-13
GO:0051704 189 Down 3.04e-08 1.01e-06
GO:0044403 157 Down 1.04e-07 3.23e-06
GO:0044419 157 Down 1.04e-07 3.23e-06
GO:0065008 149 Down 1.23e-07 3.69e-06
GO:0051701 147 Down 1.97e-07 5.74e-06
GO:0050896 291 Down 7.09e-05 2.01e-03
GO:0006096 17 Down 2.70e-04 7.43e-03
GO:0044724 24 Down 3.80e-04 9.90e-03
GO:0016052 24 Down 3.80e-04 9.90e-03
GO:0006457 72 Down 4.29e-04 1.09e-02
GO:0019319 6 Down 2.54e-03 6.06e-02
GO:0046364 6 Down 2.54e-03 6.06e-02
GO:0050789 380 Down 2.58e-03 6.06e-02
GO:0006094 5 Down 2.74e-03 6.28e-02
GO:0044723 42 Down 3.60e-03 8.07e-02
GO:0050794 359 Down 4.64e-03 1.02e-01
GO:0070682 6 Down 5.41e-03 1.16e-01
GO:0065007 401 Down 6.25e-03 1.29e-01
GO:0016485 10 Down 6.38e-03 1.29e-01
GO:0006006 12 Down 6.45e-03 1.29e-01
GO:0019318 14 Down 6.69e-03 1.29e-01
GO:0005996 14 Down 6.69e-03 1.29e-01
GO:0016051 12 Down 9.52e-03 1.80e-01
GO:0005975 53 Down 1.03e-02 1.91e-01
GO:0016255 4 Up 1.06e-02 1.93e-01
GO:0051604 12 Down 1.18e-02 2.06e-01
GO:0006497 18 Up 1.22e-02 2.06e-01
GO:0042158 18 Up 1.22e-02 2.06e-01
GO:0042157 18 Up 1.22e-02 2.06e-01
GO:0031123 8 Up 1.50e-02 2.49e-01
GO:0007275 6 Up 1.54e-02 2.51e-01
GO:0006506 9 Up 1.62e-02 2.61e-01
GO:0042176 3 Down 1.65e-02 2.61e-01
GO:0042026 3 Down 1.69e-02 2.61e-01
GO:0000375 64 Down 1.74e-02 2.61e-01
GO:0001817 3 Down 1.79e-02 2.61e-01
GO:0051239 3 Down 1.79e-02 2.61e-01
GO:0009396 4 Down 1.80e-02 2.61e-01
GO:0031167 2 Down 1.81e-02 2.61e-01
GO:0006643 15 Up 1.84e-02 2.61e-01
GO:0051051 3 Up 2.04e-02 2.85e-01
GO:0044712 59 Down 2.10e-02 2.87e-01
GO:0008380 81 Down 2.12e-02 2.87e-01
GO:0046467 13 Up 2.20e-02 2.94e-01
GO:0000245 9 Down 2.22e-02 2.94e-01
GO:0006505 10 Up 2.26e-02 2.94e-01
GO:0051276 43 Down 2.35e-02 3.03e-01
GO:0022613 98 Down 2.42e-02 3.05e-01
GO:0044767 11 Up 2.44e-02 3.05e-01
GO:0006661 10 Up 2.85e-02 3.52e-01
GO:0032312 2 Up 2.91e-02 3.55e-01
GO:0071900 3 Up 3.02e-02 3.57e-01
GO:0000079 3 Up 3.02e-02 3.57e-01
GO:0044707 7 Up 3.04e-02 3.57e-01
GO:0035383 7 Up 3.11e-02 3.57e-01
GO:0006637 7 Up 3.11e-02 3.57e-01
GO:0009247 12 Up 3.20e-02 3.63e-01
GO:0016571 5 Down 3.24e-02 3.63e-01
GO:0000377 59 Down 3.44e-02 3.77e-01
GO:0000398 59 Down 3.44e-02 3.77e-01
GO:0008154 1 Down 3.55e-02 3.84e-01
GO:0009206 8 Up 3.63e-02 3.84e-01
GO:0009201 8 Up 3.63e-02 3.84e-01
GO:0022616 5 Up 3.77e-02 3.90e-01
GO:0006271 5 Up 3.77e-02 3.90e-01
GO:0051188 30 Up 3.84e-02 3.94e-01
GO:0006664 13 Up 3.94e-02 4.00e-01
GO:1901575 165 Down 4.23e-02 4.25e-01
GO:0009056 171 Down 4.31e-02 4.29e-01
GO:0032502 12 Up 4.58e-02 4.47e-01
GO:0006084 5 Up 4.59e-02 4.47e-01
GO:0043543 15 Up 4.91e-02 4.53e-01
GO:0031399 5 Up 5.04e-02 4.53e-01
GO:0001932 5 Up 5.04e-02 4.53e-01
GO:0042325 5 Up 5.04e-02 4.53e-01
GO:0000910 4 Up 5.07e-02 4.53e-01
GO:0071826 31 Down 5.20e-02 4.53e-01
GO:0032507 2 Up 5.29e-02 4.53e-01
GO:0051651 2 Up 5.29e-02 4.53e-01
GO:0071616 4 Up 5.39e-02 4.53e-01
GO:0006085 4 Up 5.39e-02 4.53e-01
GO:0006086 4 Up 5.39e-02 4.53e-01
GO:0035384 4 Up 5.39e-02 4.53e-01
GO:0006465 7 Down 5.45e-02 4.53e-01
GO:0046148 6 Up 5.54e-02 4.53e-01
GO:0033014 6 Up 5.54e-02 4.53e-01
GO:0006783 6 Up 5.54e-02 4.53e-01
GO:0006779 6 Up 5.54e-02 4.53e-01
GO:0071840 251 Down 5.54e-02 4.53e-01
GO:0002098 4 Up 5.60e-02 4.53e-01
GO:0002097 4 Up 5.60e-02 4.53e-01
GO:0006206 6 Down 5.74e-02 4.61e-01
GO:0044085 153 Down 6.23e-02 4.91e-01
GO:0032501 8 Up 6.24e-02 4.91e-01
GO:0006511 71 Down 6.47e-02 4.91e-01
GO:0009152 17 Up 6.53e-02 4.91e-01
GO:0006098 9 Down 6.67e-02 4.91e-01
GO:0046365 9 Down 6.67e-02 4.91e-01
GO:0006740 9 Down 6.67e-02 4.91e-01
GO:0006007 9 Down 6.67e-02 4.91e-01
GO:0006739 9 Down 6.67e-02 4.91e-01
GO:0019320 9 Down 6.67e-02 4.91e-01
GO:0030154 7 Up 6.69e-02 4.91e-01
GO:0018394 4 Up 6.91e-02 4.91e-01
GO:0006475 4 Up 6.91e-02 4.91e-01
GO:0018393 4 Up 6.91e-02 4.91e-01
GO:0016573 4 Up 6.91e-02 4.91e-01
GO:0032784 3 Down 6.96e-02 4.91e-01
GO:0019362 10 Down 7.02e-02 4.91e-01
GO:0046496 10 Down 7.02e-02 4.91e-01
GO:0043933 107 Down 7.11e-02 4.93e-01
GO:0006090 24 Down 7.24e-02 4.98e-01
GO:0022618 29 Down 7.30e-02 4.99e-01
GO:0009628 22 Down 7.36e-02 5.00e-01
GO:0010608 25 Down 7.79e-02 5.23e-01
GO:0042254 80 Down 7.84e-02 5.23e-01
GO:0045017 17 Up 7.87e-02 5.23e-01
GO:0031338 14 Up 8.21e-02 5.31e-01
GO:0006890 6 Up 8.25e-02 5.31e-01
GO:0019941 73 Down 8.29e-02 5.31e-01
GO:0043632 73 Down 8.29e-02 5.31e-01
GO:0009060 17 Up 8.51e-02 5.31e-01
GO:0006099 17 Up 8.51e-02 5.31e-01
GO:0006813 4 Up 8.61e-02 5.31e-01
GO:0051603 76 Down 8.70e-02 5.31e-01
GO:0044257 76 Down 8.70e-02 5.31e-01
GO:0045859 4 Up 8.71e-02 5.31e-01
GO:0051338 4 Up 8.71e-02 5.31e-01
GO:0043549 4 Up 8.71e-02 5.31e-01
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GO:0009966 21 Up 9.66e-01 9.85e-01
GO:0016458 3 Down 9.69e-01 9.85e-01
GO:0072511 6 Down 9.70e-01 9.85e-01
GO:0070838 6 Down 9.70e-01 9.85e-01
GO:0030048 4 Up 9.70e-01 9.85e-01
GO:0046039 18 Down 9.74e-01 9.88e-01
GO:0018130 152 Down 9.75e-01 9.88e-01
GO:0006308 4 Up 9.75e-01 9.88e-01
GO:0072527 15 Up 9.78e-01 9.89e-01
GO:0006888 20 Up 9.91e-01 9.99e-01
GO:0006607 3 Down 9.92e-01 9.99e-01
GO:0046903 5 Up 9.93e-01 9.99e-01
GO:0006887 5 Up 9.93e-01 9.99e-01
GO:0032940 5 Up 9.93e-01 9.99e-01
GO:0007034 5 Down 9.93e-01 9.99e-01
GO:0043952 5 Down 9.94e-01 9.99e-01
GO:0006221 7 Up 9.96e-01 9.99e-01
GO:0009432 2 Down 9.98e-01 9.99e-01
GO:0000096 3 Up 9.98e-01 9.99e-01
GO:1901362 155 Up 9.99e-01 9.99e-01

Now KEGG pathway enrichment again making use of mroast and camera.

indices <- ids2indices(kegg.gene.sets, rownames(v2))
keg_mr <- mroast(v2, index = indices, design = modRUV, contrast = 2, nrot = 10000, set.statistic = "floormean")
keg_cam <- camera(v2, index = indices, design = modRUV, contrast = 2)

keg_mr$PValue <- format(keg_mr$PValue, scientific = TRUE, digits = 3)
keg_mr$FDR <- format(keg_mr$FDR, scientific = TRUE, digits = 3)
keg_mr$PValue.Mixed <- format(keg_mr$PValue.Mixed, scientific = TRUE, digits = 3)
keg_mr$FDR.Mixed <- format(keg_mr$FDR.Mixed, scientific = TRUE, digits = 3)
kable(keg_mr, digits = 3)
NGenes PropDown PropUp Direction PValue FDR PValue.Mixed FDR.Mixed
ec00250__PK__KEGG 12 0.250 0.000 Down 3.30e-03 9.75e-02 1.30e-02 2.82e-02
ec00740__PK__KEGG 8 0.375 0.500 Up 3.60e-03 9.75e-02 4.00e-04 1.53e-02
ec00710__PK__KEGG 10 0.600 0.000 Down 4.00e-03 9.75e-02 6.10e-03 2.04e-02
ec00280__PK__KEGG 8 0.125 0.500 Up 4.50e-03 9.75e-02 4.80e-03 1.85e-02
ec00600__PK__KEGG 11 0.091 0.545 Up 5.30e-03 9.75e-02 4.00e-03 1.72e-02
ec00650__PK__KEGG 18 0.056 0.444 Up 5.60e-03 9.75e-02 9.40e-03 2.37e-02
ec00010__PK__KEGG 25 0.440 0.080 Down 7.00e-03 9.75e-02 4.20e-03 1.74e-02
ec00562__PK__KEGG 18 0.278 0.111 Down 8.70e-03 9.75e-02 6.40e-03 2.04e-02
ec00020__PK__KEGG 18 0.111 0.389 Up 8.90e-03 9.75e-02 2.10e-03 1.53e-02
ec00380__PK__KEGG 61 0.180 0.246 Up 9.00e-03 9.75e-02 2.30e-03 1.53e-02
ec00565__PK__KEGG 24 0.208 0.292 Up 1.22e-02 9.96e-02 8.00e-04 1.53e-02
ec00561__PK__KEGG 15 0.133 0.200 Up 1.32e-02 9.96e-02 3.80e-03 1.72e-02
ec00591__PK__KEGG 7 0.286 0.143 Down 1.39e-02 9.96e-02 3.10e-03 1.72e-02
ec00230__PK__KEGG 78 0.244 0.128 Down 1.39e-02 9.96e-02 9.00e-04 1.53e-02
ec00720__PK__KEGG 17 0.118 0.412 Up 1.79e-02 9.96e-02 8.70e-03 2.35e-02
ec00900__PK__KEGG 26 0.077 0.269 Up 1.87e-02 9.96e-02 7.00e-03 2.16e-02
ec00030__PK__KEGG 14 0.429 0.000 Down 1.95e-02 9.96e-02 2.60e-02 4.32e-02
ec00983__PK__KEGG 15 0.400 0.067 Down 2.00e-02 9.96e-02 1.24e-02 2.75e-02
ec00590__PK__KEGG 7 0.286 0.000 Down 2.06e-02 9.96e-02 1.15e-02 2.65e-02
ec00361__PK__KEGG 6 0.167 0.500 Up 2.25e-02 9.96e-02 1.08e-02 2.57e-02
ec00362__PK__KEGG 19 0.158 0.368 Up 2.44e-02 9.96e-02 1.58e-02 3.09e-02
ec00440__PK__KEGG 4 0.500 0.000 Down 2.64e-02 9.96e-02 2.62e-02 4.32e-02
ec00624__PK__KEGG 36 0.222 0.222 Up 2.76e-02 9.96e-02 1.40e-03 1.53e-02
ec00240__PK__KEGG 72 0.194 0.167 Up 2.90e-02 9.96e-02 6.00e-04 1.53e-02
ec00627__PK__KEGG 61 0.213 0.246 Up 2.94e-02 9.96e-02 1.70e-03 1.53e-02
ec00351__PK__KEGG 1 0.000 1.000 Up 2.97e-02 9.96e-02 2.97e-02 4.71e-02
ec00730__PK__KEGG 14 0.071 0.214 Up 3.03e-02 9.96e-02 4.21e-02 6.28e-02
ec00660__PK__KEGG 3 0.000 0.667 Up 3.14e-02 9.96e-02 3.29e-02 5.11e-02
ec00625__PK__KEGG 4 0.250 0.250 Down 3.25e-02 9.96e-02 2.35e-02 4.12e-02
ec00623__PK__KEGG 17 0.118 0.353 Up 3.36e-02 9.96e-02 1.17e-02 2.65e-02
ec00062__PK__KEGG 6 0.167 0.667 Up 3.40e-02 9.96e-02 1.60e-02 3.09e-02
ec00860__PK__KEGG 50 0.160 0.200 Up 3.40e-02 9.96e-02 1.09e-02 2.57e-02
ec00970__PK__KEGG 41 0.341 0.171 Down 3.52e-02 9.96e-02 7.50e-03 2.19e-02
ec00360__PK__KEGG 49 0.204 0.245 Up 3.61e-02 9.96e-02 1.20e-03 1.53e-02
ec00942__PK__KEGG 46 0.174 0.261 Up 3.76e-02 9.96e-02 4.40e-03 1.76e-02
ec00941__PK__KEGG 36 0.222 0.222 Up 3.79e-02 9.96e-02 1.30e-03 1.53e-02
ec00945__PK__KEGG 36 0.222 0.222 Up 3.84e-02 9.96e-02 1.60e-03 1.53e-02
ec00270__PK__KEGG 49 0.224 0.204 Up 3.86e-02 9.96e-02 1.90e-03 1.53e-02
ec01057__PK__KEGG 42 0.190 0.238 Up 3.93e-02 9.96e-02 3.80e-03 1.72e-02
ec00053__PK__KEGG 7 0.143 0.286 Up 3.95e-02 9.96e-02 5.30e-03 1.85e-02
ec01051__PK__KEGG 36 0.222 0.222 Up 3.99e-02 9.96e-02 2.20e-03 1.53e-02
ec00260__PK__KEGG 16 0.062 0.438 Up 4.05e-02 9.96e-02 2.10e-02 3.94e-02
ec00253__PK__KEGG 51 0.176 0.235 Up 4.05e-02 9.96e-02 3.90e-03 1.72e-02
ec00130__PK__KEGG 40 0.225 0.200 Up 4.13e-02 9.96e-02 2.20e-03 1.53e-02
ec00340__PK__KEGG 46 0.196 0.239 Up 4.14e-02 9.96e-02 3.20e-03 1.72e-02
ec00920__PK__KEGG 4 0.000 0.500 Up 4.21e-02 9.96e-02 6.63e-02 8.69e-02
ec00350__PK__KEGG 50 0.200 0.220 Up 4.39e-02 1.01e-01 2.60e-03 1.54e-02
ec00450__PK__KEGG 41 0.195 0.220 Up 4.47e-02 1.01e-01 2.00e-03 1.53e-02
ec00940__PK__KEGG 48 0.188 0.229 Up 4.72e-02 1.03e-01 2.10e-03 1.53e-02
ec00981__PK__KEGG 38 0.184 0.237 Up 4.77e-02 1.03e-01 5.30e-03 1.85e-02
ec00903__PK__KEGG 16 0.188 0.312 Up 4.83e-02 1.03e-01 1.62e-02 3.09e-02
ec00965__PK__KEGG 12 0.083 0.417 Up 5.48e-02 1.14e-01 4.89e-02 7.19e-02
ec00480__PK__KEGG 25 0.200 0.280 Up 5.59e-02 1.14e-01 2.50e-03 1.54e-02
ec00910__PK__KEGG 6 0.167 0.000 Down 5.74e-02 1.14e-01 7.78e-02 9.41e-02
ec00564__PK__KEGG 53 0.151 0.264 Up 5.82e-02 1.14e-01 7.70e-03 2.19e-02
ec00310__PK__KEGG 40 0.225 0.275 Up 6.08e-02 1.14e-01 5.30e-03 1.85e-02
ec00603__PK__KEGG 1 0.000 1.000 Up 6.13e-02 1.14e-01 6.13e-02 8.69e-02
ec00592__PK__KEGG 9 0.222 0.222 Down 6.29e-02 1.14e-01 6.40e-03 2.04e-02
ec00522__PK__KEGG 1 0.000 1.000 Up 6.37e-02 1.14e-01 6.37e-02 8.69e-02
ec00513__PK__KEGG 1 0.000 1.000 Up 6.40e-02 1.14e-01 6.40e-02 8.69e-02
ec00944__PK__KEGG 1 0.000 1.000 Up 6.43e-02 1.14e-01 6.43e-02 8.69e-02
ec00604__PK__KEGG 1 0.000 1.000 Up 6.50e-02 1.14e-01 6.50e-02 8.69e-02
ec00512__PK__KEGG 1 0.000 1.000 Up 6.78e-02 1.15e-01 6.78e-02 8.69e-02
ec00906__PK__KEGG 13 0.154 0.385 Up 6.78e-02 1.15e-01 1.62e-02 3.09e-02
ec00601__PK__KEGG 1 0.000 1.000 Up 6.88e-02 1.15e-01 6.88e-02 8.71e-02
ec00626__PK__KEGG 13 0.154 0.308 Up 7.59e-02 1.25e-01 2.99e-02 4.71e-02
ec00982__PK__KEGG 3 0.333 0.333 Down 7.68e-02 1.25e-01 3.92e-02 5.93e-02
ec00630__PK__KEGG 9 0.111 0.444 Up 7.96e-02 1.27e-01 1.35e-02 2.87e-02
ec00680__PK__KEGG 24 0.208 0.292 Up 8.24e-02 1.27e-01 9.70e-03 2.39e-02
ec00950__PK__KEGG 48 0.167 0.229 Up 8.29e-02 1.27e-01 8.90e-03 2.35e-02
ec00330__PK__KEGG 27 0.074 0.296 Up 8.44e-02 1.27e-01 1.40e-02 2.92e-02
ec00966__PK__KEGG 3 0.333 0.333 Down 8.49e-02 1.27e-01 2.68e-02 4.35e-02
ec00140__PK__KEGG 3 0.333 0.333 Down 8.60e-02 1.27e-01 2.47e-02 4.20e-02
ec00540__PK__KEGG 11 0.091 0.364 Up 8.63e-02 1.27e-01 7.69e-02 9.41e-02
ec00300__PK__KEGG 19 0.158 0.211 Up 8.81e-02 1.28e-01 2.14e-02 3.94e-02
ec00622__PK__KEGG 4 0.250 0.500 Up 9.24e-02 1.31e-01 9.10e-03 2.35e-02
ec00231__PK__KEGG 11 0.091 0.364 Up 9.29e-02 1.31e-01 5.69e-02 8.26e-02
ec00930__PK__KEGG 7 0.143 0.429 Up 9.76e-02 1.36e-01 1.05e-01 1.25e-01
ec00790__PK__KEGG 9 0.222 0.222 Down 1.00e-01 1.37e-01 4.00e-03 1.72e-02
ec00770__PK__KEGG 8 0.000 0.250 Up 1.02e-01 1.37e-01 1.24e-01 1.43e-01
ec00904__PK__KEGG 12 0.167 0.333 Up 1.04e-01 1.37e-01 2.44e-02 4.20e-02
ec00071__PK__KEGG 18 0.278 0.333 Up 1.05e-01 1.37e-01 2.22e-02 3.96e-02
ec00281__PK__KEGG 4 0.250 0.500 Up 1.05e-01 1.37e-01 6.70e-02 8.69e-02
ec00670__PK__KEGG 7 0.000 0.429 Up 1.05e-01 1.37e-01 1.38e-01 1.56e-01
ec00642__PK__KEGG 13 0.154 0.308 Up 1.07e-01 1.37e-01 6.74e-02 8.69e-02
ec00785__PK__KEGG 2 0.000 0.500 Up 1.10e-01 1.40e-01 1.66e-01 1.85e-01
ec00640__PK__KEGG 17 0.118 0.294 Up 1.45e-01 1.81e-01 7.60e-03 2.19e-02
ec00364__PK__KEGG 6 0.167 0.333 Up 1.46e-01 1.81e-01 1.11e-01 1.30e-01
ec00830__PK__KEGG 5 0.200 0.200 Down 1.49e-01 1.83e-01 2.18e-02 3.95e-02
ec00510__PK__KEGG 3 0.000 0.333 Up 1.56e-01 1.87e-01 2.28e-01 2.46e-01
ec00620__PK__KEGG 23 0.174 0.174 Up 1.58e-01 1.87e-01 8.90e-03 2.35e-02
ec00563__PK__KEGG 7 0.000 0.429 Up 1.58e-01 1.87e-01 1.87e-01 2.05e-01
ec00051__PK__KEGG 20 0.150 0.150 Down 1.71e-01 2.01e-01 1.61e-02 3.09e-02
ec00040__PK__KEGG 6 0.000 0.333 Up 1.87e-01 2.17e-01 3.29e-01 3.41e-01
ec00960__PK__KEGG 18 0.167 0.222 Up 2.29e-01 2.62e-01 6.31e-02 8.69e-02
ec00908__PK__KEGG 2 0.000 0.500 Up 2.33e-01 2.64e-01 7.42e-02 9.20e-02
ec00363__PK__KEGG 6 0.167 0.167 Down 2.37e-01 2.66e-01 3.40e-02 5.21e-02
ec00061__PK__KEGG 9 0.222 0.222 Up 2.62e-01 2.91e-01 7.86e-02 9.41e-02
ec01056__PK__KEGG 3 0.000 0.333 Up 2.84e-01 3.12e-01 4.18e-01 4.26e-01
ec00500__PK__KEGG 5 0.200 0.200 Down 2.97e-01 3.23e-01 1.27e-01 1.45e-01
ec00760__PK__KEGG 12 0.083 0.250 Up 3.00e-01 3.24e-01 1.53e-01 1.72e-01
ec00633__PK__KEGG 4 0.000 0.500 Up 3.08e-01 3.29e-01 2.83e-01 2.99e-01
ec00400__PK__KEGG 8 0.000 0.250 Up 3.15e-01 3.33e-01 4.61e-01 4.65e-01
ec00410__PK__KEGG 4 0.000 0.250 Down 3.50e-01 3.67e-01 7.43e-02 9.20e-02
ec00750__PK__KEGG 2 0.000 0.000 Up 4.55e-01 4.72e-01 4.06e-01 4.18e-01
ec00780__PK__KEGG 13 0.154 0.077 Up 5.11e-01 5.26e-01 1.94e-01 2.12e-01
ec00052__PK__KEGG 8 0.125 0.125 Down 5.80e-01 5.91e-01 2.81e-01 2.99e-01
ec00520__PK__KEGG 21 0.095 0.143 Down 5.86e-01 5.91e-01 3.03e-01 3.18e-01
ec00521__PK__KEGG 5 0.000 0.000 Down 6.06e-01 6.06e-01 8.40e-01 8.40e-01

Also test using limma’s camera

keg_cam$PValue <- format(keg_cam$PValue, scientific = TRUE, digits = 3)
keg_cam$FDR <- format(keg_cam$FDR, scientific = TRUE, digits = 3)
kable(keg_cam, digits = 3)
NGenes Direction PValue FDR
ec00710__PK__KEGG 10 Down 2.10e-03 2.29e-01
ec00010__PK__KEGG 25 Down 4.86e-03 2.65e-01
ec00600__PK__KEGG 11 Up 2.59e-02 6.94e-01
ec00250__PK__KEGG 12 Down 2.85e-02 6.94e-01
ec00900__PK__KEGG 26 Up 4.18e-02 6.94e-01
ec00650__PK__KEGG 18 Up 4.36e-02 6.94e-01
ec00030__PK__KEGG 14 Down 4.87e-02 6.94e-01
ec00440__PK__KEGG 4 Down 5.64e-02 6.94e-01
ec00983__PK__KEGG 15 Down 5.73e-02 6.94e-01
ec00020__PK__KEGG 18 Up 7.10e-02 7.25e-01
ec00920__PK__KEGG 4 Up 7.43e-02 7.25e-01
ec00562__PK__KEGG 18 Down 8.85e-02 7.25e-01
ec00720__PK__KEGG 17 Up 1.20e-01 7.25e-01
ec00965__PK__KEGG 12 Up 1.45e-01 7.25e-01
ec00260__PK__KEGG 16 Up 1.50e-01 7.25e-01
ec00565__PK__KEGG 24 Up 1.68e-01 7.25e-01
ec00280__PK__KEGG 8 Up 1.77e-01 7.25e-01
ec00730__PK__KEGG 14 Up 1.85e-01 7.25e-01
ec00660__PK__KEGG 3 Up 1.87e-01 7.25e-01
ec00670__PK__KEGG 7 Up 1.92e-01 7.25e-01
ec00351__PK__KEGG 1 Up 1.93e-01 7.25e-01
ec00860__PK__KEGG 50 Up 2.10e-01 7.25e-01
ec00601__PK__KEGG 1 Up 2.20e-01 7.25e-01
ec00944__PK__KEGG 1 Up 2.20e-01 7.25e-01
ec00522__PK__KEGG 1 Up 2.20e-01 7.25e-01
ec00513__PK__KEGG 1 Up 2.20e-01 7.25e-01
ec00603__PK__KEGG 1 Up 2.20e-01 7.25e-01
ec00604__PK__KEGG 1 Up 2.20e-01 7.25e-01
ec00512__PK__KEGG 1 Up 2.20e-01 7.25e-01
ec00361__PK__KEGG 6 Up 2.26e-01 7.25e-01
ec00942__PK__KEGG 46 Up 2.31e-01 7.25e-01
ec00770__PK__KEGG 8 Up 2.32e-01 7.25e-01
ec00590__PK__KEGG 7 Down 2.38e-01 7.25e-01
ec00540__PK__KEGG 11 Up 2.40e-01 7.25e-01
ec00062__PK__KEGG 6 Up 2.42e-01 7.25e-01
ec00910__PK__KEGG 6 Down 2.46e-01 7.25e-01
ec00623__PK__KEGG 17 Up 2.49e-01 7.25e-01
ec00563__PK__KEGG 7 Up 2.53e-01 7.25e-01
ec00561__PK__KEGG 15 Up 2.69e-01 7.46e-01
ec00362__PK__KEGG 19 Up 2.86e-01 7.46e-01
ec00510__PK__KEGG 3 Up 3.12e-01 7.46e-01
ec00380__PK__KEGG 61 Up 3.19e-01 7.46e-01
ec00564__PK__KEGG 53 Up 3.29e-01 7.46e-01
ec00740__PK__KEGG 8 Up 3.30e-01 7.46e-01
ec00633__PK__KEGG 4 Up 3.46e-01 7.46e-01
ec00760__PK__KEGG 12 Up 3.48e-01 7.46e-01
ec00930__PK__KEGG 7 Up 3.57e-01 7.46e-01
ec00040__PK__KEGG 6 Up 3.58e-01 7.46e-01
ec00970__PK__KEGG 41 Down 3.68e-01 7.46e-01
ec00906__PK__KEGG 13 Up 3.69e-01 7.46e-01
ec01057__PK__KEGG 42 Up 3.76e-01 7.46e-01
ec00981__PK__KEGG 38 Up 3.78e-01 7.46e-01
ec00627__PK__KEGG 61 Up 3.83e-01 7.46e-01
ec00253__PK__KEGG 51 Up 3.84e-01 7.46e-01
ec00642__PK__KEGG 13 Up 4.05e-01 7.46e-01
ec01056__PK__KEGG 3 Up 4.10e-01 7.46e-01
ec00340__PK__KEGG 46 Up 4.15e-01 7.46e-01
ec00940__PK__KEGG 48 Up 4.19e-01 7.46e-01
ec00625__PK__KEGG 4 Down 4.30e-01 7.46e-01
ec00231__PK__KEGG 11 Up 4.41e-01 7.46e-01
ec00230__PK__KEGG 78 Down 4.49e-01 7.46e-01
ec00785__PK__KEGG 2 Up 4.50e-01 7.46e-01
ec00626__PK__KEGG 13 Up 4.74e-01 7.46e-01
ec00903__PK__KEGG 16 Up 4.77e-01 7.46e-01
ec00591__PK__KEGG 7 Down 4.77e-01 7.46e-01
ec00950__PK__KEGG 48 Up 4.79e-01 7.46e-01
ec00630__PK__KEGG 9 Up 4.82e-01 7.46e-01
ec00400__PK__KEGG 8 Up 4.91e-01 7.46e-01
ec00350__PK__KEGG 50 Up 4.94e-01 7.46e-01
ec00360__PK__KEGG 49 Up 5.09e-01 7.46e-01
ec00364__PK__KEGG 6 Up 5.17e-01 7.46e-01
ec01051__PK__KEGG 36 Up 5.23e-01 7.46e-01
ec00281__PK__KEGG 4 Up 5.31e-01 7.46e-01
ec00750__PK__KEGG 2 Up 5.36e-01 7.46e-01
ec00061__PK__KEGG 9 Up 5.36e-01 7.46e-01
ec00450__PK__KEGG 41 Up 5.44e-01 7.46e-01
ec00053__PK__KEGG 7 Up 5.46e-01 7.46e-01
ec00904__PK__KEGG 12 Up 5.46e-01 7.46e-01
ec00982__PK__KEGG 3 Down 5.58e-01 7.46e-01
ec00330__PK__KEGG 27 Up 5.61e-01 7.46e-01
ec00966__PK__KEGG 3 Down 5.79e-01 7.46e-01
ec00140__PK__KEGG 3 Down 5.79e-01 7.46e-01
ec00624__PK__KEGG 36 Up 5.81e-01 7.46e-01
ec00521__PK__KEGG 5 Down 5.88e-01 7.46e-01
ec00941__PK__KEGG 36 Up 5.89e-01 7.46e-01
ec00945__PK__KEGG 36 Up 5.89e-01 7.46e-01
ec00071__PK__KEGG 18 Up 6.42e-01 8.04e-01
ec00480__PK__KEGG 25 Up 6.91e-01 8.50e-01
ec00830__PK__KEGG 5 Down 7.12e-01 8.50e-01
ec00908__PK__KEGG 2 Up 7.15e-01 8.50e-01
ec00960__PK__KEGG 18 Up 7.17e-01 8.50e-01
ec00310__PK__KEGG 40 Up 7.26e-01 8.50e-01
ec00300__PK__KEGG 19 Up 7.31e-01 8.50e-01
ec00130__PK__KEGG 40 Up 7.33e-01 8.50e-01
ec00500__PK__KEGG 5 Down 7.44e-01 8.53e-01
ec00240__PK__KEGG 72 Up 7.73e-01 8.78e-01
ec00780__PK__KEGG 13 Up 7.95e-01 8.86e-01
ec00640__PK__KEGG 17 Up 7.97e-01 8.86e-01
ec00270__PK__KEGG 49 Up 8.28e-01 9.12e-01
ec00520__PK__KEGG 21 Down 8.39e-01 9.14e-01
ec00051__PK__KEGG 20 Down 8.51e-01 9.14e-01
ec00680__PK__KEGG 24 Up 8.55e-01 9.14e-01
ec00622__PK__KEGG 4 Up 8.71e-01 9.22e-01
ec00620__PK__KEGG 23 Up 8.90e-01 9.30e-01
ec00363__PK__KEGG 6 Down 9.00e-01 9.30e-01
ec00790__PK__KEGG 9 Down 9.05e-01 9.30e-01
ec00410__PK__KEGG 4 Down 9.15e-01 9.32e-01
ec00052__PK__KEGG 8 Down 9.27e-01 9.35e-01
ec00592__PK__KEGG 9 Down 9.51e-01 9.51e-01

Gene sets from Daily et al and Shock et al

We now test using roast and camera for deregulation of gene sets obtained from the papers:

Daily, J. P., D. Scanfeld, N. Pochet, K. Le Roch, D. Plouffe, M. Kamal, O. Sarr, et al. 2007. “Distinct Physiological States of Plasmodium Falciparum in Malaria-Infected Patients.” Nature 450 (7172): 1091–95.

Shock, Jennifer L., Kael F. Fischer, and Joseph L. DeRisi. 2007. “Whole-Genome Analysis of mRNA Decay in Plasmodium Falciparum Reveals a Global Lengthening of mRNA Half-Life during the Intra-Erythrocytic Development Cycle.” Genome Biology 8 (7): R134.

setwd(wd)

# Load gene lists from Daily et al and Shock et al
daily_figure2 <- fread("./data/daily_expression_figure2.csv", data.table = FALSE, header = TRUE)

JLshock <- c("PF3D7_0320800", "PF3D7_0410400", "PF3D7_0507600", "PF3D7_0520300", "PF3D7_0720000", "PF3D7_0811300", "PF3D7_0819900", "PF3D7_0909400", "PF3D7_0909900", 
    "PF3D7_1006100", "PF3D7_1032100", "PF3D7_1103800", "PF3D7_1106300", "PF3D7_1107000", "PF3D7_1124400", "PF3D7_1128600", "PF3D7_1209200", "PF3D7_1224300", 
    "PF3D7_1235300", "PF3D7_1307000", "PF3D7_1308900", "PF3D7_1325000", "PF3D7_1340100", "PF3D7_1364500", "PF3D7_1427800", "PF3D7_1443300", "PF3D7_1443500", 
    "PF3D7_1449700", "PF3D7_0519500")

# Load entrex geneID mappings
entrez_geneID_mappings <- fread("./data/geneID_mappings.txt", data.table = FALSE, stringsAsFactors = FALSE)

upcluster2 <- daily_figure2$Gene[daily_figure2$`Up regulated in Cluster 2?` == "Y"]
upcluster1 <- daily_figure2$Gene[daily_figure2$`Up regulated in Cluster 2?` == "N"]
glycolisis <- daily_figure2$Gene[daily_figure2$type == "Glycolisis"]
tricarboxylic <- daily_figure2$Gene[daily_figure2$type == "Tricarboxylic acid cycle"]
fatty_acid <- daily_figure2$Gene[daily_figure2$type == "Fatty acid metabolism"]

upcluster2 <- as.vector(geneID_mappings$current[geneID_mappings$old %in% upcluster2])
upcluster1 <- as.vector(geneID_mappings$current[geneID_mappings$old %in% upcluster1])
glycolisis <- as.vector(geneID_mappings$current[geneID_mappings$old %in% glycolisis])
tricarboxylic <- as.vector(geneID_mappings$current[geneID_mappings$old %in% tricarboxylic])
fatty_acid <- as.vector(geneID_mappings$current[geneID_mappings$old %in% fatty_acid])

indices <- ids2indices(list(up_in_starvation = upcluster1, up_int_vitro = upcluster2, glycolisis = glycolisis, tricarboxylic = tricarboxylic, fatty_acid = fatty_acid, 
    mRNA_degradation = JLshock), rownames(v2$E))
mroast(v2, index = indices, design = modRUV, contrast = 2, nrot = 10000, set.statistic = "floormean")
##                  NGenes  PropDown     PropUp Direction     PValue        FDR PValue.Mixed  FDR.Mixed
## up_int_vitro         12 0.8333333 0.00000000      Down 0.01129887 0.02812219   0.01249875 0.01493851
## glycolisis           19 0.5789474 0.05263158      Down 0.01309869 0.02812219   0.01009899 0.01493851
## mRNA_degradation     29 0.2758621 0.06896552      Down 0.01459854 0.02812219   0.00769923 0.01493851
## tricarboxylic        11 0.1818182 0.36363636        Up 0.01879812 0.02812219   0.00129987 0.00749925
## up_in_starvation     33 0.1818182 0.21212121        Up 0.06249375 0.07493251   0.00929907 0.01493851
## fatty_acid           17 0.1764706 0.11764706        Up 0.12558744 0.12558744   0.07129287 0.07129287
camera(v2, index = indices, design = modRUV, contrast = 2)
##                  NGenes Direction       PValue          FDR
## up_int_vitro         12      Down 1.470968e-05 8.825807e-05
## glycolisis           19      Down 1.322405e-03 3.967216e-03
## mRNA_degradation     29      Down 8.826335e-02 1.765267e-01
## up_in_starvation     33        Up 2.390539e-01 3.166989e-01
## tricarboxylic        11        Up 2.639157e-01 3.166989e-01
## fatty_acid           17        Up 3.466823e-01 3.466823e-01

System Information

setwd(wd)
sessionInfo()
## R version 3.4.3 (2017-11-30)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: OS X El Capitan 10.11.6
## 
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
## 
## attached base packages:
##  [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] pheatmap_1.0.8             knitr_1.17                 stringr_1.2.0              dplyr_0.7.4                data.table_1.10.4-3       
##  [6] VennDiagram_1.6.18         futile.logger_1.4.3        RColorBrewer_1.1-2         EDASeq_2.10.0              ShortRead_1.34.2          
## [11] GenomicAlignments_1.12.2   SummarizedExperiment_1.6.5 DelayedArray_0.2.7         matrixStats_0.52.2         Rsamtools_1.28.0          
## [16] GenomicRanges_1.28.6       GenomeInfoDb_1.12.3        Biostrings_2.44.2          XVector_0.16.0             IRanges_2.10.5            
## [21] S4Vectors_0.14.7           BiocParallel_1.10.1        Biobase_2.36.2             BiocGenerics_0.22.1        reshape2_1.4.3            
## [26] ggplot2_2.2.1              ruv_0.9.6                  quadprog_1.5-5             edgeR_3.18.1               limma_3.32.10             
## 
## loaded via a namespace (and not attached):
##  [1] bit64_0.9-7             splines_3.4.3           R.utils_2.6.0           assertthat_0.2.0        statmod_1.4.30          highr_0.6              
##  [7] aroma.light_3.6.0       latticeExtra_0.6-28     blob_1.1.0              GenomeInfoDbData_0.99.0 yaml_2.1.16             RSQLite_2.0            
## [13] backports_1.1.2         lattice_0.20-35         glue_1.2.0              digest_0.6.13           colorspace_1.3-2        htmltools_0.3.6        
## [19] Matrix_1.2-12           R.oo_1.21.0             plyr_1.8.4              pkgconfig_2.0.1         XML_3.98-1.9            biomaRt_2.32.1         
## [25] genefilter_1.58.1       zlibbioc_1.22.0         xtable_1.8-2            scales_0.5.0            tibble_1.3.4            annotate_1.54.0        
## [31] GenomicFeatures_1.28.5  lazyeval_0.2.1          survival_2.41-3         magrittr_1.5            memoise_1.1.0           evaluate_0.10.1        
## [37] R.methodsS3_1.7.1       hwriter_1.3.2           tools_3.4.3             formatR_1.5             munsell_0.4.3           locfit_1.5-9.1         
## [43] bindrcpp_0.2            lambda.r_1.2            AnnotationDbi_1.38.2    compiler_3.4.3          DESeq_1.28.0            rlang_0.1.6            
## [49] RCurl_1.95-4.8          labeling_0.3            bitops_1.0-6            rmarkdown_1.8           gtable_0.2.0            DBI_0.7                
## [55] R6_2.2.2                rtracklayer_1.36.6      bit_1.1-12              bindr_0.1               rprojroot_1.3-1         futile.options_1.0.0   
## [61] stringi_1.1.6           Rcpp_0.12.14            geneplotter_1.54.0